diff --git a/.github/workflows/__export-file-baseline-information.yml b/.github/workflows/__export-file-baseline-information.yml
index 4ce8b40285..acdb099087 100644
--- a/.github/workflows/__export-file-baseline-information.yml
+++ b/.github/workflows/__export-file-baseline-information.yml
@@ -124,4 +124,5 @@ jobs:
     env:
       CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
       CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
+      CODEQL_ACTION_PER_LANGUAGE_BUNDLES: false
       CODEQL_ACTION_TEST_MODE: true
diff --git a/lib/entry-points.js b/lib/entry-points.js
index ad7ac988a1..9b1949238d 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -172086,7 +172086,7 @@ var featureConfig = {
     envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_SKIP_RESOURCE_CHECKS",
     minimumVersion: void 0
   },
-  ["per_language_bundles" /* PerLanguageBundles */]: {
+  ["per_language_bundles_v2" /* PerLanguageBundles */]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_PER_LANGUAGE_BUNDLES",
     minimumVersion: void 0
@@ -173213,6 +173213,13 @@ async function loadRepositoryProperties(repositoryNwo, logger2) {
 }
 
 // src/config/db-config.ts
+var defaultSuites = /* @__PURE__ */ new Set([
+  "security-experimental",
+  "security-extended",
+  "security-and-quality",
+  "code-quality",
+  "code-scanning"
+]);
 var ORG_SCHEMA = {
   /** An array of model pack names. */
   "model-packs": optional(array(string))
@@ -173226,12 +173233,21 @@ var DEFAULT_SETUP_CONFIG_SCHEMA = {
     object(DEFAULT_SETUP_SCHEMA)
   )
 };
+function checkDefaultSetupConfig(config) {
+  return checkSchema(DEFAULT_SETUP_CONFIG_SCHEMA, config);
+}
+function matchesDefaultSetupConfigSchema(config) {
+  if (!isObject2(config)) {
+    return false;
+  }
+  const result = checkDefaultSetupConfig(config);
+  return result.valid && result.unknownKeys.length === 0;
+}
 function mergeDefaultSetupAndUserConfigs(logger2, fromConfigInput, fromConfigFile) {
   logger2.debug(
     "Combining configuration files from 'config' and 'config-file' inputs"
   );
-  const schemaCheckResult = checkSchema(
-    DEFAULT_SETUP_CONFIG_SCHEMA,
+  const schemaCheckResult = checkDefaultSetupConfig(
     fromConfigInput
   );
   if (schemaCheckResult.invalidKeys.length > 0) {
@@ -173388,52 +173404,41 @@ async function calculateAugmentation(rawPacksInput, rawQueriesInput, repositoryP
     languages,
     packsInputCombines
   );
-  const queriesInputCombines = shouldCombine(rawQueriesInput);
-  const queriesInput = parseQueriesFromInput(
-    rawQueriesInput,
-    queriesInputCombines
+  const queries = parseQueriesFromInput(rawQueriesInput);
+  const repoPropertyQueries = parseQueriesFromInput(
+    repositoryProperties["github-codeql-extra-queries" /* EXTRA_QUERIES */],
+    "github-codeql-extra-queries" /* EXTRA_QUERIES */
   );
-  const repoExtraQueries = repositoryProperties["github-codeql-extra-queries" /* EXTRA_QUERIES */];
-  const repoExtraQueriesCombines = shouldCombine(repoExtraQueries);
-  const repoPropertyQueries = {
-    combines: repoExtraQueriesCombines,
-    input: parseQueriesFromInput(
-      repoExtraQueries,
-      repoExtraQueriesCombines,
-      new ConfigurationError(
-        getRepoPropertyError(
-          "github-codeql-extra-queries" /* EXTRA_QUERIES */,
-          getEmptyCombinesError()
-        )
-      )
-    )
-  };
   return {
     packsInputCombines,
     packsInput: packsInput?.[languages[0]],
-    queriesInput,
-    queriesInputCombines,
+    queriesInput: queries.input,
+    queriesInputCombines: queries.combines,
     repoPropertyQueries
   };
 }
-function parseQueriesFromInput(rawQueriesInput, queriesInputCombines, errorToThrow) {
-  if (!rawQueriesInput) {
-    return void 0;
+function parseQueriesFromInput(value, repositoryProperty) {
+  const combines = shouldCombine(value);
+  if (!value) {
+    return { combines, input: void 0 };
   }
-  const trimmedInput = queriesInputCombines ? rawQueriesInput.trim().slice(1).trim() : rawQueriesInput?.trim() ?? "";
-  if (queriesInputCombines && trimmedInput.length === 0) {
-    if (errorToThrow) {
-      throw errorToThrow;
-    }
+  const trimmedInput = combines ? value.trim().slice(1).trim() : value.trim();
+  if (combines && trimmedInput.length === 0) {
     throw new ConfigurationError(
-      getConfigFilePropertyError(
+      repositoryProperty !== void 0 ? getRepoPropertyError(
+        repositoryProperty,
+        getEmptyCombinesError()
+      ) : getConfigFilePropertyError(
         void 0,
         "queries",
         "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs."
       )
     );
   }
-  return trimmedInput.split(",").map((query) => ({ uses: query.trim() }));
+  return {
+    combines,
+    input: trimmedInput.split(",").map((query) => ({ uses: query.trim() }))
+  };
 }
 function combineQueries(logger2, config, augmentationProperties) {
   const result = [];
@@ -174815,20 +174820,22 @@ async function applyIncrementalAnalysisSettings(config, hasDiffRanges, codeql, l
     });
   }
 }
-async function determineUserConfig(action, tempDir, inputs) {
-  const validateConfig = await action.features.getValue(
-    "validate_db_config" /* ValidateDbConfig */
+async function parseConfigInput({ logger: logger2, features }, configInput) {
+  if (configInput === void 0) {
+    return void 0;
+  }
+  return parseUserConfig(
+    logger2,
+    "`config` input",
+    configInput,
+    await features.getValue("validate_db_config" /* ValidateDbConfig */)
   );
-  if (inputs.configInput) {
+}
+async function determineUserConfig(action, tempDir, inputs) {
+  if (inputs.configInput !== void 0) {
     const computedConfigPath = userConfigFromActionPath(tempDir);
     const allowMergeConfigs = () => action.features.getValue("allow_merge_config_files" /* AllowMergeConfigFiles */);
     if (inputs.configFile && isDefaultSetup(action.env) && await allowMergeConfigs()) {
-      const fromConfigInput = parseUserConfig(
-        action.logger,
-        "`config` input",
-        inputs.configInput,
-        validateConfig
-      );
       const fromConfigFile = await loadUserConfig(
         action,
         inputs.configFile,
@@ -174838,7 +174845,7 @@ async function determineUserConfig(action, tempDir, inputs) {
       );
       const mergedConfig = mergeDefaultSetupAndUserConfigs(
         action.logger,
-        fromConfigInput,
+        inputs.configInput,
         fromConfigFile
       );
       fs10.writeFileSync(computedConfigPath, dump(mergedConfig));
@@ -174853,11 +174860,12 @@ async function determineUserConfig(action, tempDir, inputs) {
           `Both a config file and config input were provided. Ignoring config file.`
         );
       }
-      fs10.writeFileSync(computedConfigPath, inputs.configInput);
+      fs10.writeFileSync(computedConfigPath, dump(inputs.configInput));
       inputs.configFile = computedConfigPath;
       action.logger.debug(
         `Using config from action input: ${inputs.configFile}`
       );
+      return inputs.configInput;
     }
   }
   if (!inputs.configFile) {
@@ -175561,6 +175569,33 @@ var PER_LANGUAGE_BUNDLE_LANGUAGES = {
   ["osx64" /* Osx64 */]: /* @__PURE__ */ new Set(["swift" /* swift */]),
   ["win64" /* Win64 */]: /* @__PURE__ */ new Set()
 };
+function getOtherLanguagePacksReason(inputs) {
+  if (inputs.configFile !== void 0) {
+    return `the configuration file '${inputs.configFile}' may use queries that need library packs for other languages`;
+  }
+  if (inputs.configInput !== void 0 && !matchesDefaultSetupConfigSchema(inputs.configInput)) {
+    return "the 'config' input may use queries that need library packs for other languages";
+  }
+  const query = findNonBuiltInQuery(
+    parseQueriesFromInput(inputs.queriesInput).input
+  );
+  if (query !== void 0) {
+    return `the query '${query}' from the 'queries' input may need library packs for other languages`;
+  }
+  const extraQuery = findNonBuiltInQuery(
+    parseQueriesFromInput(
+      inputs.extraQueriesProperty,
+      "github-codeql-extra-queries" /* EXTRA_QUERIES */
+    ).input
+  );
+  if (extraQuery !== void 0) {
+    return `the query '${extraQuery}' from the '${"github-codeql-extra-queries" /* EXTRA_QUERIES */}' repository property may need library packs for other languages`;
+  }
+  return void 0;
+}
+function findNonBuiltInQuery(queries) {
+  return queries?.find((query) => !defaultSuites.has(query.uses))?.uses;
+}
 async function getPerLanguageBundleLanguage({
   env,
   features,
@@ -175568,6 +175603,7 @@ async function getPerLanguageBundleLanguage({
 }, options) {
   const {
     rawLanguages,
+    otherLanguagePacksReason,
     cliVersion: cliVersion2,
     compressionMethod,
     platform: platform2,
@@ -175578,8 +175614,11 @@ async function getPerLanguageBundleLanguage({
     logger2.debug(`Not using a per-language CodeQL bundle since ${reason}.`);
     return void 0;
   };
-  if (!await features.getValue("per_language_bundles" /* PerLanguageBundles */)) {
-    return explain(`the ${"per_language_bundles" /* PerLanguageBundles */} feature is disabled`);
+  if (!await features.getValue("per_language_bundles_v2" /* PerLanguageBundles */)) {
+    return explain("the feature is disabled");
+  }
+  if (otherLanguagePacksReason !== void 0) {
+    return explain(otherLanguagePacksReason);
   }
   if (rawLanguages?.length !== 1) {
     return explain(
@@ -176212,7 +176251,7 @@ async function resolveDefaultCliVersion(defaultCliVersion, rawLanguages, useOver
   }
   return defaultCliVersion.enabledVersions[0];
 }
-async function getCodeQLSource(toolsInput, defaultCliVersion, rawLanguages, useOverlayAwareDefaultCliVersion, apiDetails, variant, tarSupportsZstd, features, logger2) {
+async function getCodeQLSource(toolsInput, defaultCliVersion, rawLanguages, otherLanguagePacksReason, useOverlayAwareDefaultCliVersion, apiDetails, variant, tarSupportsZstd, features, logger2) {
   if (toolsInput && !isReservedToolsValue(toolsInput) && !toolsInput.startsWith("http")) {
     logger2.info(`Using CodeQL CLI from local path ${toolsInput}`);
     const compressionMethod2 = inferCompressionMethod(toolsInput);
@@ -176265,6 +176304,7 @@ async function getCodeQLSource(toolsInput, defaultCliVersion, rawLanguages, useO
     bundle = await getLatestNightlyBundle(
       { env: getEnv(), features, logger: logger2 },
       rawLanguages,
+      otherLanguagePacksReason,
       variant
     );
     toolsInput = bundle.url;
@@ -176432,6 +176472,7 @@ async function getCodeQLSource(toolsInput, defaultCliVersion, rawLanguages, useO
       { env: getEnv(), features, logger: logger2 },
       {
         rawLanguages,
+        otherLanguagePacksReason,
         cliVersion: cliVersion2,
         compressionMethod,
         platform: platform2,
@@ -176595,7 +176636,7 @@ function getCanonicalToolcacheVersion(cliVersion2, bundleVersion2, logger2) {
   }
   return cliVersion2;
 }
-async function setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, useOverlayAwareDefaultCliVersion, features, logger2) {
+async function setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, otherLanguagePacksReason, useOverlayAwareDefaultCliVersion, features, logger2) {
   if (!await isBinaryAccessible("tar", logger2)) {
     throw new ConfigurationError(
       "Could not find tar in PATH, so unable to extract CodeQL bundle."
@@ -176606,6 +176647,7 @@ async function setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, defau
     toolsInput,
     defaultCliVersion,
     rawLanguages,
+    otherLanguagePacksReason,
     useOverlayAwareDefaultCliVersion,
     apiDetails,
     variant,
@@ -176704,7 +176746,7 @@ async function useZstdBundle(cliVersion2, tarSupportsZstd) {
 function getTempExtractionDir(tempDir) {
   return path13.join(tempDir, v4_default());
 }
-async function getLatestNightlyBundle(action, rawLanguages, variant) {
+async function getLatestNightlyBundle(action, rawLanguages, otherLanguagePacksReason, variant) {
   const { logger: logger2 } = action;
   const zstdAvailability = await isZstdAvailable(logger2);
   const compressionMethod = await useZstdBundle(
@@ -176714,6 +176756,7 @@ async function getLatestNightlyBundle(action, rawLanguages, variant) {
   const platform2 = getBundlePlatform();
   const language = await getPerLanguageBundleLanguage(action, {
     rawLanguages,
+    otherLanguagePacksReason,
     cliVersion: void 0,
     compressionMethod,
     platform: platform2,
@@ -176854,7 +176897,7 @@ function isDiskConfigurationError(e) {
     e.message.includes("EACCES")
   );
 }
-async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, useOverlayAwareDefaultCliVersion, features, logger2, checkVersion) {
+async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, otherLanguagePacksReason, useOverlayAwareDefaultCliVersion, features, logger2, checkVersion) {
   try {
     const {
       codeqlFolder,
@@ -176868,6 +176911,7 @@ async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliV
       variant,
       defaultCliVersion,
       rawLanguages,
+      otherLanguagePacksReason,
       useOverlayAwareDefaultCliVersion,
       features,
       logger2
@@ -177967,13 +178011,6 @@ ${extensionContents}`
   );
   return diffRangeDir;
 }
-var defaultSuites = /* @__PURE__ */ new Set([
-  "security-experimental",
-  "security-extended",
-  "security-and-quality",
-  "code-quality",
-  "code-scanning"
-]);
 function resolveQuerySuiteAlias(language, maybeSuite) {
   if (defaultSuites.has(maybeSuite)) {
     return `${language}-${maybeSuite}.qls`;
@@ -179506,7 +179543,7 @@ var core15 = __toESM(require_core());
 var toolrunner4 = __toESM(require_toolrunner());
 var github3 = __toESM(require_github());
 var io6 = __toESM(require_io());
-async function initCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, useOverlayAwareDefaultCliVersion, features, logger2) {
+async function initCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, rawLanguages, otherLanguagePacksReason, useOverlayAwareDefaultCliVersion, features, logger2) {
   logger2.startGroup("Setup CodeQL tools");
   const { codeql, toolsDownloadStatusReport, toolsSource, toolsVersion } = await setupCodeQL(
     toolsInput,
@@ -179515,6 +179552,7 @@ async function initCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVe
     variant,
     defaultCliVersion,
     rawLanguages,
+    otherLanguagePacksReason,
     useOverlayAwareDefaultCliVersion,
     features,
     logger2,
@@ -179876,6 +179914,8 @@ async function combineSarifFilesUsingCLI(sarifFiles, gitHubVersion, features, lo
       codeQLDefaultVersionInfo,
       void 0,
       // rawLanguages: upload-lib does not run analysis
+      void 0,
+      // otherLanguagePacksReason: upload-lib does not run analysis
       false,
       // useOverlayAwareDefaultCliVersion: upload-lib does not run analysis
       features,
@@ -186330,6 +186370,17 @@ async function run3(actionState) {
     const rawLanguages = getRawLanguagesNoAutodetect(
       getOptionalInput("languages")
     );
+    const configInput = await parseConfigInput(
+      actionStateWithFeatures,
+      getOptionalInput("config")
+    );
+    const queriesInput = getOptionalInput("queries");
+    const otherLanguagePacksReason = getOtherLanguagePacksReason({
+      configFile,
+      configInput,
+      queriesInput,
+      extraQueriesProperty: repositoryProperties["github-codeql-extra-queries" /* EXTRA_QUERIES */]
+    });
     const useOverlayAwareDefaultCliVersion = analysisKinds?.length === 1 && analysisKinds[0] === "code-scanning" /* CodeScanning */;
     const initCodeQLResult = await initCodeQL(
       toolsInput?.value,
@@ -186338,6 +186389,7 @@ async function run3(actionState) {
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
+      otherLanguagePacksReason,
       useOverlayAwareDefaultCliVersion,
       features,
       logger2
@@ -186376,13 +186428,13 @@ async function run3(actionState) {
     config = await initConfig2(actionStateWithFeatures, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
-      queriesInput: getOptionalInput("queries"),
+      queriesInput,
       packsInput: getOptionalInput("packs"),
       buildModeInput: getOptionalInput("build-mode"),
       ramInput: getOptionalInput("ram"),
       configFile,
       dbLocation: getOptionalInput("db-location"),
-      configInput: getOptionalInput("config"),
+      configInput,
       dependencyCachingEnabled: getDependencyCachingEnabled(),
       // Debug mode is enabled if:
       // - The `init` Action is passed `debug: true`.
@@ -187342,6 +187394,11 @@ async function run6(actionState) {
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
+      // CodeQL resolves the dependencies of queries that aren't in compiled packs from the bundle,
+      // so the queries that the workflow runs with this CLI may need library packs for languages
+      // other than those in the `languages` input. That input therefore only informs the choice of
+      // CLI version.
+      "the 'setup-codeql' Action can't tell whether the queries that the workflow runs will need library packs for other languages",
       analysisKinds.length === 1 && analysisKinds[0] === "code-scanning" /* CodeScanning */,
       features,
       logger2
diff --git a/pr-checks/checks/export-file-baseline-information.yml b/pr-checks/checks/export-file-baseline-information.yml
index c5d5d12dda..ce22ec5d5f 100644
--- a/pr-checks/checks/export-file-baseline-information.yml
+++ b/pr-checks/checks/export-file-baseline-information.yml
@@ -11,6 +11,10 @@ installDotNet: true
 env:
   CODEQL_ACTION_SKIP_FILE_COVERAGE_ON_PRS: false
   CODEQL_ACTION_SUBLANGUAGE_FILE_COVERAGE: true
+  # To balance speed and coverage, we analyze only a single language (JavaScript), but use the
+  # combined bundle so we can test that baseline information is reported for each language in the
+  # multi-language source directory.
+  CODEQL_ACTION_PER_LANGUAGE_BUNDLES: false
 steps:
   - uses: ./../action/init
     id: init
diff --git a/setup-codeql/action.yml b/setup-codeql/action.yml
index 8d13eeaff0..14083b4f95 100644
--- a/setup-codeql/action.yml
+++ b/setup-codeql/action.yml
@@ -21,19 +21,16 @@ inputs:
     required: false
   languages:
     description: >-
-      A comma-separated list of CodeQL languages that will be analyzed in subsequent
-      `github/codeql-action/init` and `github/codeql-action/analyze` invocations. If specified, the
-      Action may use this list to select a CodeQL CLI version that is best suited to analyzing those
-      languages, for example by preferring a version that has a cached overlay-base database for the
-      specified languages. This input is not remembered and must also be passed to
-      `github/codeql-action/init`.
+      A comma-separated list of CodeQL languages that the installed CodeQL CLI will be used to
+      analyze. If specified, the Action may use this list to select a CodeQL CLI version that is
+      best suited to analyzing those languages, for example by preferring a version that has a
+      cached overlay-base database for the specified languages.
     required: false
   analysis-kinds:
     description: >-
-      [Internal] A comma-separated list of analysis kinds that subsequent
-      `github/codeql-action/init` invocations will enable. If specified, the Action may use this
-      list to select a CodeQL CLI version that is best suited to those analysis kinds. This input is
-      not remembered and must also be passed to `github/codeql-action/init`.
+      [Internal] A comma-separated list of analysis kinds that the installed CodeQL CLI will be used
+      for. If specified, the Action may use this list to select a CodeQL CLI version that is best
+      suited to those analysis kinds.
 
       Available options are the same as for the `analysis-kinds` input on the `init` Action.
     default: 'code-scanning'
diff --git a/src/analyze.test.ts b/src/analyze.test.ts
index 7523d239bf..80fc7a5474 100644
--- a/src/analyze.test.ts
+++ b/src/analyze.test.ts
@@ -7,12 +7,12 @@ import * as sinon from "sinon";
 import { CodeQuality, CodeScanning, RiskAssessment } from "./analyses";
 import {
   runQueries,
-  defaultSuites,
   resolveQuerySuiteAlias,
   addSarifExtension,
   diffRangeExtensionPackContents,
 } from "./analyze";
 import { createStubCodeQL } from "./codeql";
+import { defaultSuites } from "./config/db-config";
 import { Feature } from "./feature-flags";
 import { BuiltInLanguage } from "./languages";
 import { getRunnerLogger } from "./logging";
diff --git a/src/analyze.ts b/src/analyze.ts
index 8f90711682..d585fd6d83 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -9,6 +9,7 @@ import { getTemporaryDirectory } from "./actions-util";
 import * as analyses from "./analyses";
 import { setupCppAutobuild } from "./autobuild";
 import { type CodeQL } from "./codeql";
+import { defaultSuites } from "./config/db-config";
 import * as configUtils from "./config-utils";
 import {
   getCsharpTempDependencyDir,
@@ -357,15 +358,6 @@ dataExtensions:
   return diffRangeDir;
 }
 
-// A set of default query suite names that are understood by the CLI.
-export const defaultSuites: Set<string> = new Set([
-  "security-experimental",
-  "security-extended",
-  "security-and-quality",
-  "code-quality",
-  "code-scanning",
-]);
-
 /**
  * If `maybeSuite` is the name of a default query suite, it is resolved into the corresponding
  * query suite name for the given `language`. Otherwise, `maybeSuite` is returned as is.
diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index 5f2eb31156..3237d57723 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -99,6 +99,7 @@ async function installIntoToolcache({
       ? { enabledVersions: [{ cliVersion, tagName }] }
       : SAMPLE_DEFAULT_CLI_VERSION,
     undefined, // rawLanguages
+    undefined, // otherLanguagePacksReason
     false, // useOverlayAwareDefaultCliVersion
     createFeatures([]),
     getRunnerLogger(true),
@@ -172,6 +173,7 @@ test.serial(
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
@@ -207,6 +209,7 @@ test.serial(
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
@@ -246,6 +249,7 @@ test.serial(
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
@@ -355,6 +359,7 @@ for (const {
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
@@ -397,6 +402,7 @@ for (const toolcacheVersion of [
           util.GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           features,
           getRunnerLogger(true),
@@ -441,6 +447,7 @@ test.serial(
           ],
         },
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
@@ -487,6 +494,7 @@ test.serial(
           ],
         },
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
@@ -526,6 +534,7 @@ test.serial(
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
@@ -567,6 +576,7 @@ test.serial(
         util.GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         getRunnerLogger(true),
diff --git a/src/codeql.ts b/src/codeql.ts
index a4da8ad68a..6df604e394 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -302,6 +302,9 @@ export function isDiskConfigurationError(e: unknown): boolean {
  * @param variant
  * @param defaultCliVersion
  * @param rawLanguages Raw set of languages.
+ * @param otherLanguagePacksReason Why the CodeQL CLI may need packs for languages other than
+ *   `rawLanguages`, or `undefined` if it won't. If defined, the combined bundle is used. See
+ *   `PerLanguageBundleOptions.otherLanguagePacksReason`.
  * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
  * @param features Information about the features that are enabled.
  * @param logger
@@ -316,6 +319,7 @@ export async function setupCodeQL(
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
   useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
@@ -339,6 +343,7 @@ export async function setupCodeQL(
       variant,
       defaultCliVersion,
       rawLanguages,
+      otherLanguagePacksReason,
       useOverlayAwareDefaultCliVersion,
       features,
       logger,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 29d72f3af4..3ea71ebc42 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -473,6 +473,9 @@ const simpleConfigFileContents = `
   queries:
     - uses: ./foo_file`;
 
+/** The configuration in `simpleConfigFileContents`, as parsed from the `config` input. */
+const simpleConfigInput = yaml.load(simpleConfigFileContents) as UserConfig;
+
 /** A less minimal configuration file. */
 const otherConfigFileContents = `
   name: my config
@@ -591,7 +594,7 @@ test.serial(
         createTestInitConfigInputs({
           languagesInput,
           configFile: configFilePath,
-          configInput,
+          configInput: yaml.load(configInput) as UserConfig,
           tempDir,
           codeql,
           workspacePath: tempDir,
@@ -2343,6 +2346,40 @@ test("applyIncrementalAnalysisSettings: adds exclusions for diff-informed-only r
   ]);
 });
 
+test("parseConfigInput - returns undefined when the input isn't set", async (t) => {
+  await callee(configUtils.parseConfigInput)
+    .withArgs(undefined)
+    .passes(t.is, undefined);
+});
+
+test("parseConfigInput - parses the input as YAML", async (t) => {
+  await callee(configUtils.parseConfigInput)
+    .withArgs(simpleConfigFileContents)
+    .passes(t.deepEqual, {
+      name: "my config",
+      queries: [{ uses: "./foo_file" }],
+    });
+});
+
+test("parseConfigInput - throws a ConfigurationError naming the input if it isn't valid YAML", async (t) => {
+  await callee(configUtils.parseConfigInput)
+    .withArgs("queries: [")
+    .throws(t, {
+      instanceOf: ConfigurationError,
+      message: /^Cannot parse "`config` input"/,
+    });
+});
+
+test("parseConfigInput - throws a ConfigurationError naming the input if validation fails", async (t) => {
+  await callee(configUtils.parseConfigInput)
+    .withFeatures([Feature.ValidateDbConfig])
+    .withArgs("queries: 1")
+    .throws(t, {
+      instanceOf: ConfigurationError,
+      message: /^The configuration file "`config` input" is invalid/,
+    });
+});
+
 test("determineUserConfig - empty config when neither input is specified", async (t) => {
   await withTmpDir(async (tmpDir) => {
     const target = callee(configUtils.determineUserConfig)
@@ -2413,7 +2450,7 @@ test("determineUserConfig - loads config input", async (t) => {
     const expectedConfigPath = configUtils.userConfigFromActionPath(tmpDir);
 
     const inputs = createTestInitConfigInputs({
-      configInput: simpleConfigFileContents,
+      configInput: simpleConfigInput,
       configFile: undefined,
       workspacePath: tmpDir,
     });
@@ -2423,17 +2460,15 @@ test("determineUserConfig - loads config input", async (t) => {
 
     await target
       // The input source and path of the generated config file should have been logged.
-      .logs(
-        t,
-        "Using config from action input:",
-        `Using configuration file: ${expectedConfigPath}`,
-      )
-      // The message about no configuration input and
-      // the warning about both inputs should not have been logged.
+      .logs(t, `Using config from action input: ${expectedConfigPath}`)
+      // The message about no configuration input and the warning about both inputs should not have
+      // been logged. The generated config file isn't loaded, since the `config` input has already
+      // been parsed.
       .notLogs(
         t,
         "No configuration file was provided",
         "Both a config file and config input were provided. Ignoring config file.",
+        `Using configuration file: ${expectedConfigPath}`,
       )
       // The loaded configuration should match `simpleConfigFileContents`.
       .passes(t.deepEqual, {
@@ -2452,7 +2487,7 @@ test("determineUserConfig - ignores config file input when both specified", asyn
     const expectedConfigPath = configUtils.userConfigFromActionPath(tmpDir);
 
     const inputs = createTestInitConfigInputs({
-      configInput: simpleConfigFileContents,
+      configInput: simpleConfigInput,
       configFile: configFilePath,
       workspacePath: tmpDir,
     });
@@ -2466,10 +2501,14 @@ test("determineUserConfig - ignores config file input when both specified", asyn
       .logs(
         t,
         `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
         "Both a config file and config input were provided. Ignoring config file.",
       )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
       // The loaded configuration should match `simpleConfigFileContents`.
       .passes(t.deepEqual, {
         name: "my config",
@@ -2481,12 +2520,12 @@ test("determineUserConfig - ignores config file input when both specified", asyn
   });
 });
 
-/** A `config` input that we might get from Default Setup. */
-const defaultSetupConfigInput = `
+/** The configuration from a `config` input that we might get from Default Setup. */
+const defaultSetupConfigInput = yaml.load(`
   threat-models: [local, remote]
   default-setup:
     org:
-      model-packs: [foo, bar]`;
+      model-packs: [foo, bar]`) as UserConfig;
 
 test("determineUserConfig - merges configs if FF is enabled in Default Setup", async (t) => {
   await withTmpDir(async (tmpDir) => {
@@ -2555,7 +2594,7 @@ test("determineUserConfig - ignores config file input in Default Setup if FF is
       .withArgs(
         tmpDir,
         createTestInitConfigInputs({
-          configInput: simpleConfigFileContents,
+          configInput: simpleConfigInput,
           configFile: configFilePath,
           workspacePath: tmpDir,
         }),
@@ -2565,10 +2604,14 @@ test("determineUserConfig - ignores config file input in Default Setup if FF is
       .logs(
         t,
         `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
         "Both a config file and config input were provided. Ignoring config file.",
       )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
       .passes(t.deepEqual, {
         name: "my config",
         queries: [{ uses: "./foo_file" }],
@@ -2587,7 +2630,7 @@ test("determineUserConfig - ignores config file input outside Default Setup if F
       .withArgs(
         tmpDir,
         createTestInitConfigInputs({
-          configInput: simpleConfigFileContents,
+          configInput: simpleConfigInput,
           configFile: configFilePath,
           workspacePath: tmpDir,
         }),
@@ -2597,10 +2640,14 @@ test("determineUserConfig - ignores config file input outside Default Setup if F
       .logs(
         t,
         `Using config from action input: ${expectedConfigPath}`,
-        `Using configuration file: ${expectedConfigPath}`,
         "Both a config file and config input were provided. Ignoring config file.",
       )
-      .notLogs(t, "No configuration file was provided")
+      // The generated config file isn't loaded, since the `config` input has already been parsed.
+      .notLogs(
+        t,
+        "No configuration file was provided",
+        `Using configuration file: ${expectedConfigPath}`,
+      )
       .passes(t.deepEqual, {
         name: "my config",
         queries: [{ uses: "./foo_file" }],
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 4dd14b2909..ba15138dcc 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -337,7 +337,8 @@ export interface InitConfigInputs {
   packsInput: string | undefined;
   configFile: string | undefined;
   dbLocation: string | undefined;
-  configInput: string | undefined;
+  /** The configuration from the `config` input. */
+  configInput: UserConfig | undefined;
   buildModeInput: string | undefined;
   ramInput: string | undefined;
   dependencyCachingEnabled: string | undefined;
@@ -1043,6 +1044,29 @@ export async function applyIncrementalAnalysisSettings(
   }
 }
 
+/**
+ * Parses the `config` input, which contains a configuration in YAML.
+ *
+ * @returns The configuration, or `undefined` if the input isn't set. Unless configuration validation
+ *   is enabled, the configuration might not be a mapping.
+ * @throws A `ConfigurationError` if the input isn't valid YAML or, when configuration validation is
+ *   enabled, isn't a valid configuration.
+ */
+export async function parseConfigInput(
+  { logger, features }: ActionState<["Logger", "FeatureFlags"]>,
+  configInput: string | undefined,
+): Promise<UserConfig | undefined> {
+  if (configInput === undefined) {
+    return undefined;
+  }
+  return parseUserConfig(
+    logger,
+    "`config` input",
+    configInput,
+    await features.getValue(Feature.ValidateDbConfig),
+  );
+}
+
 /**
  * Determines where to load the `UserConfig` for the CLI from and loads it.
  *
@@ -1057,17 +1081,13 @@ export async function determineUserConfig(
   tempDir: string,
   inputs: InitConfigInputs,
 ): Promise<UserConfig> {
-  const validateConfig = await action.features.getValue(
-    Feature.ValidateDbConfig,
-  );
-
   // We have the following cases:
   // 1. A `config` or `config-file` input is provided, but not both: use the provided one.
   // 2. Both are provided and we are in an advanced workflow: ignore the `config-file` input.
   // 3. Both are provided and we are in Default Setup: the `config` input uses a limited
   //    set of options, which are supported by `mergeDefaultSetupAndUserConfigs`,
   //    and we merge the two configs.
-  if (inputs.configInput) {
+  if (inputs.configInput !== undefined) {
     const computedConfigPath = userConfigFromActionPath(tempDir);
 
     // Get a function which enables us to determine whether the FF that allows us to
@@ -1084,12 +1104,6 @@ export async function determineUserConfig(
     ) {
       // If the FF is enabled and we are in Default Setup, combine the supported
       // configuration file properties and write the result to disk.
-      const fromConfigInput = parseUserConfig(
-        action.logger,
-        "`config` input",
-        inputs.configInput,
-        validateConfig,
-      );
       const fromConfigFile = await loadUserConfig(
         action,
         inputs.configFile,
@@ -1102,7 +1116,7 @@ export async function determineUserConfig(
       // the CLI or other CodeQL Action steps.
       const mergedConfig = mergeDefaultSetupAndUserConfigs(
         action.logger,
-        fromConfigInput,
+        inputs.configInput,
         fromConfigFile,
       );
       fs.writeFileSync(computedConfigPath, yaml.dump(mergedConfig));
@@ -1122,12 +1136,13 @@ export async function determineUserConfig(
         );
       }
 
-      // Write the `config` input straight to disk.
-      fs.writeFileSync(computedConfigPath, inputs.configInput);
+      // Write the `config` input to disk.
+      fs.writeFileSync(computedConfigPath, yaml.dump(inputs.configInput));
       inputs.configFile = computedConfigPath;
       action.logger.debug(
         `Using config from action input: ${inputs.configFile}`,
       );
+      return inputs.configInput;
     }
   }
 
diff --git a/src/config/db-config.test.ts b/src/config/db-config.test.ts
index 63d9d2ffec..76fa918015 100644
--- a/src/config/db-config.test.ts
+++ b/src/config/db-config.test.ts
@@ -625,3 +625,73 @@ test("mergeDefaultSetupAndUserConfigs - warns about invalid keys from Default Se
     `Invalid keys in Default Setup configuration: ${expectedInvalidKeys}`,
   ]);
 });
+
+/** Parses `contents` as a configuration without validating it. */
+function parseUnvalidatedConfig(contents: string): dbConfig.UserConfig {
+  return dbConfig.parseUserConfig(
+    getRunnerLogger(true),
+    "test",
+    contents,
+    false,
+  );
+}
+
+test("matchesDefaultSetupConfigSchema - returns true for configurations that only use Default Setup properties", (t) => {
+  for (const contents of [
+    [
+      "default-setup:",
+      "  org:",
+      "    model-packs: [ github/immutable-actions-list@0.0.1 ]",
+      "threat-models: [  ]",
+    ].join("\n"),
+    "threat-models: [ local ]",
+    "{}",
+  ]) {
+    t.true(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for configurations that use other properties", (t) => {
+  for (const contents of [
+    "queries: [ { uses: ./queries/show_ifs.ql } ]",
+    "paths-ignore: [ tests ]",
+    "default-setup: { org: { model-packs: [], queries: [] } }",
+  ]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for invalid Default Setup properties", (t) => {
+  for (const contents of [
+    "threat-models: local",
+    "default-setup: { org: { model-packs: [ 1 ] } }",
+  ]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
+
+test("matchesDefaultSetupConfigSchema - returns false for configurations that aren't mappings", (t) => {
+  for (const contents of ["- threat-models", "local", "null"]) {
+    t.false(
+      dbConfig.matchesDefaultSetupConfigSchema(
+        parseUnvalidatedConfig(contents),
+      ),
+      contents,
+    );
+  }
+});
diff --git a/src/config/db-config.ts b/src/config/db-config.ts
index 7b5bdbd8ce..eb2cf15eb7 100644
--- a/src/config/db-config.ts
+++ b/src/config/db-config.ts
@@ -33,6 +33,15 @@ export interface QuerySpec {
   uses: string;
 }
 
+// A set of default query suite names that are understood by the CLI.
+export const defaultSuites: Set<string> = new Set([
+  "security-experimental",
+  "security-extended",
+  "security-and-quality",
+  "code-quality",
+  "code-scanning",
+]);
+
 const ORG_SCHEMA = {
   /** An array of model pack names. */
   "model-packs": json.optional(json.array(json.string)),
@@ -77,7 +86,11 @@ export interface UserConfig {
   "default-setup"?: DefaultSetupConfig;
 }
 
-/** A subset of the `UserConfig` schema that is used by Default Setup. */
+/**
+ * A subset of the `UserConfig` schema that is used by Default Setup. None of these properties may
+ * add queries, since a per-language CodeQL bundle can be used with a `config` input that only sets
+ * them.
+ */
 const DEFAULT_SETUP_CONFIG_SCHEMA = {
   "threat-models": json.optional(json.array(json.string)),
   "default-setup": json.optional<DefaultSetupConfig>(
@@ -85,6 +98,31 @@ const DEFAULT_SETUP_CONFIG_SCHEMA = {
   ),
 } as const satisfies json.Schema;
 
+/**
+ * Checks `config` against the properties that Default Setup sets in the `config` input. The result
+ * lists any other properties in `unknownKeys`, and any properties with invalid values in
+ * `invalidKeys`.
+ */
+function checkDefaultSetupConfig(
+  config: json.UnvalidatedObject<any>,
+): json.CheckSchemaResult {
+  return json.checkSchema(DEFAULT_SETUP_CONFIG_SCHEMA, config);
+}
+
+/**
+ * Returns whether `config` is a mapping that only sets the properties that Default Setup sets in
+ * the `config` input, to valid values.
+ */
+export function matchesDefaultSetupConfigSchema(config: UserConfig): boolean {
+  // Unless validation is enabled, `parseUserConfig` doesn't check that the YAML is a mapping.
+  if (!json.isObject(config)) {
+    return false;
+  }
+  const result = checkDefaultSetupConfig(config as json.UnvalidatedObject<any>);
+  // `valid` doesn't account for unknown properties.
+  return result.valid && result.unknownKeys.length === 0;
+}
+
 /**
  * Merges supported properties from two configuration files. This is intended only for
  * use with merging the `config` input provided by Default Setup with a potentially
@@ -107,8 +145,7 @@ export function mergeDefaultSetupAndUserConfigs(
   // Check for unexpected keys in the configuration from the `config` input
   // that was provided by Default Setup. This should only contain the keys
   // we would expect to receive from Default Setup.
-  const schemaCheckResult = json.checkSchema(
-    DEFAULT_SETUP_CONFIG_SCHEMA,
+  const schemaCheckResult = checkDefaultSetupConfig(
     fromConfigInput as json.UnvalidatedObject<any>,
   );
 
@@ -437,63 +474,59 @@ export async function calculateAugmentation(
     languages,
     packsInputCombines,
   );
-  const queriesInputCombines = shouldCombine(rawQueriesInput);
-  const queriesInput = parseQueriesFromInput(
-    rawQueriesInput,
-    queriesInputCombines,
+  const queries = parseQueriesFromInput(rawQueriesInput);
+  const repoPropertyQueries = parseQueriesFromInput(
+    repositoryProperties[RepositoryPropertyName.EXTRA_QUERIES],
+    RepositoryPropertyName.EXTRA_QUERIES,
   );
 
-  const repoExtraQueries =
-    repositoryProperties[RepositoryPropertyName.EXTRA_QUERIES];
-  const repoExtraQueriesCombines = shouldCombine(repoExtraQueries);
-  const repoPropertyQueries = {
-    combines: repoExtraQueriesCombines,
-    input: parseQueriesFromInput(
-      repoExtraQueries,
-      repoExtraQueriesCombines,
-      new ConfigurationError(
-        errorMessages.getRepoPropertyError(
-          RepositoryPropertyName.EXTRA_QUERIES,
-          errorMessages.getEmptyCombinesError(),
-        ),
-      ),
-    ),
-  };
-
   return {
     packsInputCombines,
     packsInput: packsInput?.[languages[0]],
-    queriesInput,
-    queriesInputCombines,
+    queriesInput: queries.input,
+    queriesInputCombines: queries.combines,
     repoPropertyQueries,
   };
 }
 
-function parseQueriesFromInput(
-  rawQueriesInput: string | undefined,
-  queriesInputCombines: boolean,
-  errorToThrow?: ConfigurationError,
-) {
-  if (!rawQueriesInput) {
-    return undefined;
+/**
+ * Parses a comma-separated list of queries, which may start with '+'. `combines` is whether it
+ * starts with '+', and `input` holds the queries, or is `undefined` if `value` is unset or empty.
+ * Entries aren't validated, so an empty entry becomes `{ uses: "" }`.
+ *
+ * @param value The list of queries.
+ * @param repositoryProperty The repository property that `value` comes from, if any. Errors name
+ *   this property, or the `queries` input if it's unset.
+ * @throws A `ConfigurationError` if `value` is a '+' with no queries after it.
+ */
+export function parseQueriesFromInput(
+  value: string | undefined,
+  repositoryProperty?: RepositoryPropertyName,
+): Augmentation<QuerySpec[]> {
+  const combines = shouldCombine(value);
+  if (!value) {
+    return { combines, input: undefined };
   }
 
-  const trimmedInput = queriesInputCombines
-    ? rawQueriesInput.trim().slice(1).trim()
-    : (rawQueriesInput?.trim() ?? "");
-  if (queriesInputCombines && trimmedInput.length === 0) {
-    if (errorToThrow) {
-      throw errorToThrow;
-    }
+  const trimmedInput = combines ? value.trim().slice(1).trim() : value.trim();
+  if (combines && trimmedInput.length === 0) {
     throw new ConfigurationError(
-      errorMessages.getConfigFilePropertyError(
-        undefined,
-        "queries",
-        "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs.",
-      ),
+      repositoryProperty !== undefined
+        ? errorMessages.getRepoPropertyError(
+            repositoryProperty,
+            errorMessages.getEmptyCombinesError(),
+          )
+        : errorMessages.getConfigFilePropertyError(
+            undefined,
+            "queries",
+            "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs.",
+          ),
     );
   }
-  return trimmedInput.split(",").map((query) => ({ uses: query.trim() }));
+  return {
+    combines,
+    input: trimmedInput.split(",").map((query) => ({ uses: query.trim() })),
+  };
 }
 
 /**
diff --git a/src/feature-flags.ts b/src/feature-flags.ts
index afddaea2a4..59b50e2dfd 100644
--- a/src/feature-flags.ts
+++ b/src/feature-flags.ts
@@ -168,7 +168,7 @@ export enum Feature {
    * Controls whether we may download a bundle containing only the single language being analysed,
    * rather than the combined bundle that contains every language.
    */
-  PerLanguageBundles = "per_language_bundles",
+  PerLanguageBundles = "per_language_bundles_v2",
   QaTelemetryEnabled = "qa_telemetry_enabled",
   /** Routes (some) API requests through the registry proxy. */
   ProxyApiRequests = "proxy_api_requests",
diff --git a/src/init-action.ts b/src/init-action.ts
index 41e0b8629d..2b3c95e0ba 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -40,7 +40,10 @@ import {
 } from "./diagnostics";
 import { ActionsEnvVars, EnvVar } from "./environment";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
-import { loadRepositoryProperties } from "./feature-flags/properties";
+import {
+  loadRepositoryProperties,
+  RepositoryPropertyName,
+} from "./feature-flags/properties";
 import {
   checkInstallPython311,
   checkPacksForOverlayCompatibility,
@@ -58,6 +61,7 @@ import {
   OverlayBaseDatabaseDownloadStats,
 } from "./overlay/caching";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
+import { getOtherLanguagePacksReason } from "./per-language-bundles";
 import { getRepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import {
@@ -302,6 +306,18 @@ async function run(
     const rawLanguages = configUtils.getRawLanguagesNoAutodetect(
       getOptionalInput("languages"),
     );
+    const configInput = await configUtils.parseConfigInput(
+      actionStateWithFeatures,
+      getOptionalInput("config"),
+    );
+    const queriesInput = getOptionalInput("queries");
+    const otherLanguagePacksReason = getOtherLanguagePacksReason({
+      configFile,
+      configInput,
+      queriesInput,
+      extraQueriesProperty:
+        repositoryProperties[RepositoryPropertyName.EXTRA_QUERIES],
+    });
     const useOverlayAwareDefaultCliVersion =
       analysisKinds?.length === 1 &&
       analysisKinds[0] === AnalysisKind.CodeScanning;
@@ -312,6 +328,7 @@ async function run(
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
+      otherLanguagePacksReason,
       useOverlayAwareDefaultCliVersion,
       features,
       logger,
@@ -362,13 +379,13 @@ async function run(
     config = await initConfig(actionStateWithFeatures, {
       analysisKinds,
       languagesInput: getOptionalInput("languages"),
-      queriesInput: getOptionalInput("queries"),
+      queriesInput,
       packsInput: getOptionalInput("packs"),
       buildModeInput: getOptionalInput("build-mode"),
       ramInput: getOptionalInput("ram"),
       configFile,
       dbLocation: getOptionalInput("db-location"),
-      configInput: getOptionalInput("config"),
+      configInput,
       dependencyCachingEnabled: getDependencyCachingEnabled(),
       // Debug mode is enabled if:
       // - The `init` Action is passed `debug: true`.
diff --git a/src/init.ts b/src/init.ts
index c6a258e58c..d757e29976 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -40,6 +40,7 @@ export async function initCodeQL(
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
   useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
@@ -58,6 +59,7 @@ export async function initCodeQL(
       variant,
       defaultCliVersion,
       rawLanguages,
+      otherLanguagePacksReason,
       useOverlayAwareDefaultCliVersion,
       features,
       logger,
diff --git a/src/per-language-bundles.test.ts b/src/per-language-bundles.test.ts
index 0330b51a63..09500d2f77 100644
--- a/src/per-language-bundles.test.ts
+++ b/src/per-language-bundles.test.ts
@@ -4,9 +4,11 @@ import { ActionsEnvVars } from "./environment";
 import { Feature } from "./feature-flags";
 import { BuiltInLanguage } from "./languages";
 import {
+  getOtherLanguagePacksReason,
   getPerLanguageBundleLanguage,
   MIN_PER_LANGUAGE_BUNDLE_CLI_VERSION,
   PerLanguageBundleOptions,
+  QueryConfigInputs,
 } from "./per-language-bundles";
 import { BundlePlatform } from "./platform";
 import {
@@ -16,11 +18,12 @@ import {
   initAllState,
   LoggedMessage,
 } from "./testing-utils";
-import { GitHubVariant } from "./util";
+import { ConfigurationError, GitHubVariant } from "./util";
 
 /** Options for which we would use a per-language bundle. */
 const ELIGIBLE_OPTIONS: PerLanguageBundleOptions = {
   rawLanguages: ["java"],
+  otherLanguagePacksReason: undefined,
   // Any version at least as new as the minimum will do.
   cliVersion: MIN_PER_LANGUAGE_BUNDLE_CLI_VERSION,
   compressionMethod: "zstd",
@@ -81,6 +84,23 @@ test("getPerLanguageBundleLanguage requires a known language", async (t) => {
   t.is(await checkEligibility({ rawLanguages: ["cobol"] }), undefined);
 });
 
+test("getPerLanguageBundleLanguage explains why the CodeQL CLI may need packs for other languages before checking the languages", async (t) => {
+  // Without a language, the explanation would otherwise suggest requesting a single language.
+  for (const rawLanguages of [["java"], undefined]) {
+    const messages: LoggedMessage[] = [];
+    const language = await checkEligibility(
+      { rawLanguages, otherLanguagePacksReason: "an example reason" },
+      { logger: getRecordingLogger(messages, { logToConsole: false }) },
+    );
+
+    t.is(language, undefined);
+    t.deepEqual(
+      messages.map((message) => message.message),
+      ["Not using a per-language CodeQL bundle since an example reason."],
+    );
+  }
+});
+
 test("getPerLanguageBundleLanguage requires a zstd bundle", async (t) => {
   t.is(await checkEligibility({ compressionMethod: "gzip" }), undefined);
 });
@@ -142,9 +162,7 @@ test("getPerLanguageBundleLanguage explains a disabled feature before checking e
   t.is(language, undefined);
   t.deepEqual(
     messages.map((message) => message.message),
-    [
-      "Not using a per-language CodeQL bundle since the per_language_bundles feature is disabled.",
-    ],
+    ["Not using a per-language CodeQL bundle since the feature is disabled."],
   );
 });
 
@@ -155,6 +173,7 @@ test("getPerLanguageBundleLanguage skips only the release version check for the
   for (const overrides of [
     { rawLanguages: undefined },
     { rawLanguages: ["java", "python"] },
+    { otherLanguagePacksReason: "an example reason" },
     { compressionMethod: "gzip" as const },
     { platform: BundlePlatform.Osx64 },
     { variant: GitHubVariant.GHES },
@@ -173,3 +192,106 @@ test("getPerLanguageBundleLanguage skips only the release version check for the
     undefined,
   );
 });
+
+/** Query configuration inputs that configure nothing. */
+const NO_QUERY_CONFIG: QueryConfigInputs = {
+  configFile: undefined,
+  configInput: undefined,
+  queriesInput: undefined,
+  extraQueriesProperty: undefined,
+};
+
+test("getOtherLanguagePacksReason returns undefined when no queries are configured", (t) => {
+  t.is(getOtherLanguagePacksReason(NO_QUERY_CONFIG), undefined);
+});
+
+test("getOtherLanguagePacksReason returns undefined for built-in query suites", (t) => {
+  for (const queries of [
+    "security-extended",
+    "+security-and-quality",
+    " security-extended , code-quality ",
+  ]) {
+    t.is(
+      getOtherLanguagePacksReason({
+        ...NO_QUERY_CONFIG,
+        queriesInput: queries,
+        extraQueriesProperty: queries,
+      }),
+      undefined,
+      queries,
+    );
+  }
+});
+
+test("getOtherLanguagePacksReason returns undefined for a config input that only uses default setup properties", (t) => {
+  t.is(
+    getOtherLanguagePacksReason({
+      ...NO_QUERY_CONFIG,
+      // The configuration from the `config` input that default setup passes.
+      configInput: {
+        "default-setup": {
+          org: { "model-packs": ["github/immutable-actions-list@0.0.1"] },
+        },
+        "threat-models": [],
+      },
+    }),
+    undefined,
+  );
+});
+
+test("getOtherLanguagePacksReason explains a configuration file", (t) => {
+  t.is(
+    getOtherLanguagePacksReason({
+      ...NO_QUERY_CONFIG,
+      configFile: "./.github/codeql/codeql-config.yml",
+    }),
+    "the configuration file './.github/codeql/codeql-config.yml' may use queries that need " +
+      "library packs for other languages",
+  );
+});
+
+test("getOtherLanguagePacksReason explains a config input that uses other properties", (t) => {
+  t.is(
+    getOtherLanguagePacksReason({
+      ...NO_QUERY_CONFIG,
+      configInput: { queries: [{ uses: "./queries/show_ifs.ql" }] },
+    }),
+    "the 'config' input may use queries that need library packs for other languages",
+  );
+});
+
+test("getOtherLanguagePacksReason explains the first query in the queries input that isn't a built-in query suite", (t) => {
+  t.is(
+    getOtherLanguagePacksReason({
+      ...NO_QUERY_CONFIG,
+      queriesInput:
+        "+security-extended, ./queries/show_ifs.ql, octo-org/queries@main",
+    }),
+    "the query './queries/show_ifs.ql' from the 'queries' input may need library packs for " +
+      "other languages",
+  );
+});
+
+test("getOtherLanguagePacksReason explains a query in the extra queries repository property that isn't a built-in query suite", (t) => {
+  t.is(
+    getOtherLanguagePacksReason({
+      ...NO_QUERY_CONFIG,
+      extraQueriesProperty: "+octo-org/queries/show_ifs.ql@main",
+    }),
+    "the query 'octo-org/queries/show_ifs.ql@main' from the 'github-codeql-extra-queries' " +
+      "repository property may need library packs for other languages",
+  );
+});
+
+test("getOtherLanguagePacksReason throws a ConfigurationError for a '+' with no queries after it", (t) => {
+  // Loading the configuration would throw the same errors.
+  for (const inputs of [
+    { queriesInput: "+" },
+    { extraQueriesProperty: " + " },
+  ]) {
+    t.throws(
+      () => getOtherLanguagePacksReason({ ...NO_QUERY_CONFIG, ...inputs }),
+      { instanceOf: ConfigurationError },
+    );
+  }
+});
diff --git a/src/per-language-bundles.ts b/src/per-language-bundles.ts
index e0db649c7a..9a46d2df66 100644
--- a/src/per-language-bundles.ts
+++ b/src/per-language-bundles.ts
@@ -2,7 +2,15 @@ import * as semver from "semver";
 
 import { ActionState } from "./action-common";
 import { isGitHubHostedRunner } from "./actions-util";
+import {
+  defaultSuites,
+  matchesDefaultSetupConfigSchema,
+  parseQueriesFromInput,
+  QuerySpec,
+  UserConfig,
+} from "./config/db-config";
 import { Feature } from "./feature-flags";
+import { RepositoryPropertyName } from "./feature-flags/properties";
 import { BuiltInLanguage, parseBuiltInLanguage } from "./languages";
 import { BundlePlatform } from "./platform";
 import * as tar from "./tar";
@@ -31,10 +39,95 @@ const PER_LANGUAGE_BUNDLE_LANGUAGES: Readonly<
   [BundlePlatform.Win64]: new Set(),
 };
 
+/** Query configuration that is known before CodeQL is set up. */
+export interface QueryConfigInputs {
+  /** The configuration file from the `config-file` input or repository property. */
+  configFile: string | undefined;
+  /** The configuration from the `config` input. */
+  configInput: UserConfig | undefined;
+  /** The `queries` input. */
+  queriesInput: string | undefined;
+  /** The `github-codeql-extra-queries` repository property. */
+  extraQueriesProperty: string | undefined;
+}
+
+/**
+ * Explains why the configured queries may need library packs for languages other than the one
+ * being analyzed, which a per-language bundle doesn't contain. Returns `undefined` if the only
+ * queries that these inputs add are built-in query suites. The `packs` input doesn't matter, since
+ * query packs are downloaded together with their dependencies.
+ *
+ * Any configuration file is assumed to configure such queries, since reading it may need file or API
+ * access. So is the `config` input, unless it only sets the properties that default setup sets (see
+ * `matchesDefaultSetupConfigSchema`).
+ *
+ * @throws A `ConfigurationError` if the `queries` input or the `github-codeql-extra-queries`
+ *   repository property is a '+' with no queries after it, unless an input that's checked earlier
+ *   already gives a reason.
+ */
+export function getOtherLanguagePacksReason(
+  inputs: QueryConfigInputs,
+): string | undefined {
+  if (inputs.configFile !== undefined) {
+    return (
+      `the configuration file '${inputs.configFile}' may use queries that need library packs ` +
+      "for other languages"
+    );
+  }
+
+  // The `config` input can configure queries in the same way as a configuration file. The
+  // properties that default setup sets, listed in `DEFAULT_SETUP_CONFIG_SCHEMA` in
+  // `config/db-config.ts`, don't add queries.
+  if (
+    inputs.configInput !== undefined &&
+    !matchesDefaultSetupConfigSchema(inputs.configInput)
+  ) {
+    return "the 'config' input may use queries that need library packs for other languages";
+  }
+
+  // We can't tell which language a local query or a query from another repository is for without
+  // loading it, and CodeQL resolves the library packs for every configured query, including those
+  // for languages that aren't being analyzed.
+  const query = findNonBuiltInQuery(
+    parseQueriesFromInput(inputs.queriesInput).input,
+  );
+  if (query !== undefined) {
+    return `the query '${query}' from the 'queries' input may need library packs for other languages`;
+  }
+  const extraQuery = findNonBuiltInQuery(
+    parseQueriesFromInput(
+      inputs.extraQueriesProperty,
+      RepositoryPropertyName.EXTRA_QUERIES,
+    ).input,
+  );
+  if (extraQuery !== undefined) {
+    return (
+      `the query '${extraQuery}' from the '${RepositoryPropertyName.EXTRA_QUERIES}' repository ` +
+      "property may need library packs for other languages"
+    );
+  }
+
+  return undefined;
+}
+
+/** Returns the `uses` value of the first of `queries` that isn't a built-in query suite. */
+function findNonBuiltInQuery(
+  queries: QuerySpec[] | undefined,
+): string | undefined {
+  return queries?.find((query) => !defaultSuites.has(query.uses))?.uses;
+}
+
 /** Inputs that determine whether we may download a per-language bundle. */
 export interface PerLanguageBundleOptions {
   /** Explicit input only: autodetection needs a CLI instance. */
   rawLanguages: string[] | undefined;
+  /**
+   * Why the CodeQL CLI may need packs for other languages, for example because of the configured
+   * queries, or `undefined` if it won't. If defined, the combined bundle is used, and this reason is
+   * logged to complete the sentence "Not using a per-language CodeQL bundle since ...". See
+   * `getOtherLanguagePacksReason`.
+   */
+  otherLanguagePacksReason: string | undefined;
   /** Requested CLI version, if known. Ignored when requesting the latest nightly. */
   cliVersion: string | undefined;
   compressionMethod: tar.CompressionMethod;
@@ -56,6 +149,7 @@ export async function getPerLanguageBundleLanguage(
 ): Promise<BuiltInLanguage | undefined> {
   const {
     rawLanguages,
+    otherLanguagePacksReason,
     cliVersion,
     compressionMethod,
     platform,
@@ -69,7 +163,14 @@ export async function getPerLanguageBundleLanguage(
   };
 
   if (!(await features.getValue(Feature.PerLanguageBundles))) {
-    return explain(`the ${Feature.PerLanguageBundles} feature is disabled`);
+    return explain("the feature is disabled");
+  }
+
+  // A defined reason means the CodeQL CLI may need packs for other languages, for example because
+  // of the configured queries. That applies whichever languages were requested, so check it first
+  // to avoid suggesting that requesting a single language would be enough.
+  if (otherLanguagePacksReason !== undefined) {
+    return explain(otherLanguagePacksReason);
   }
 
   if (rawLanguages?.length !== 1) {
diff --git a/src/setup-codeql-action.ts b/src/setup-codeql-action.ts
index 91666f19cd..23a9c65ebd 100644
--- a/src/setup-codeql-action.ts
+++ b/src/setup-codeql-action.ts
@@ -165,6 +165,12 @@ async function run(
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
+      // CodeQL resolves the dependencies of queries that aren't in compiled packs from the bundle,
+      // so the queries that the workflow runs with this CLI may need library packs for languages
+      // other than those in the `languages` input. That input therefore only informs the choice of
+      // CLI version.
+      "the 'setup-codeql' Action can't tell whether the queries that the workflow runs will need " +
+        "library packs for other languages",
       analysisKinds.length === 1 &&
         analysisKinds[0] === AnalysisKind.CodeScanning,
       features,
diff --git a/src/setup-codeql.test.ts b/src/setup-codeql.test.ts
index c33ac0700a..3fef11e63e 100644
--- a/src/setup-codeql.test.ts
+++ b/src/setup-codeql.test.ts
@@ -157,6 +157,7 @@ test.serial(
         url,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -242,6 +243,7 @@ for (const {
           "linked",
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           SAMPLE_DOTCOM_API_DETAILS,
           GitHubVariant.DOTCOM,
@@ -275,6 +277,7 @@ test.serial(
         "latest",
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -320,6 +323,7 @@ test.serial(
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         logger,
@@ -377,6 +381,7 @@ test.serial(
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         logger,
@@ -425,6 +430,7 @@ test.serial(
         "nightly",
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -452,6 +458,7 @@ test.serial(
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         ["javascript"],
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         features,
         logger,
@@ -495,6 +502,7 @@ test.serial(
         undefined,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -550,6 +558,7 @@ for (const bundlePath of [
           GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           createFeatures([]),
           getRecordingLogger(messages),
@@ -603,6 +612,7 @@ test.serial(
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         createFeatures([Feature.CleanupToolcacheBundles]),
         getRunnerLogger(true),
@@ -636,6 +646,7 @@ for (const toolsInput of ["nightly", "nightly-latest"]) {
           toolsInput,
           SAMPLE_DEFAULT_CLI_VERSION,
           ["java"],
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           SAMPLE_DOTCOM_API_DETAILS,
           GitHubVariant.DOTCOM,
@@ -671,12 +682,23 @@ test.serial(
 
     await withTmpDir(async (tmpDir) => {
       setupActionsVars(tmpDir, tmpDir);
-      for (const { languages, features } of [
+      for (const { languages, otherLanguagePacksReason, features } of [
         // The per-language feature is disabled.
-        { languages: ["java"], features: createFeatures([]) },
+        {
+          languages: ["java"],
+          otherLanguagePacksReason: undefined,
+          features: createFeatures([]),
+        },
         // More than one language requires a combined bundle.
         {
           languages: ["java", "python"],
+          otherLanguagePacksReason: undefined,
+          features: createFeatures([Feature.PerLanguageBundles]),
+        },
+        // The configured queries may need library packs for other languages.
+        {
+          languages: ["java"],
+          otherLanguagePacksReason: "an example reason",
           features: createFeatures([Feature.PerLanguageBundles]),
         },
       ]) {
@@ -684,6 +706,7 @@ test.serial(
           "nightly",
           SAMPLE_DEFAULT_CLI_VERSION,
           languages,
+          otherLanguagePacksReason,
           false, // useOverlayAwareDefaultCliVersion
           SAMPLE_DOTCOM_API_DETAILS,
           GitHubVariant.DOTCOM,
@@ -718,6 +741,7 @@ for (const perLanguageBundles of [false, true]) {
           undefined, // toolsInput: the nightly is selected by ForceNightly
           SAMPLE_DEFAULT_CLI_VERSION,
           ["java"],
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           SAMPLE_DOTCOM_API_DETAILS,
           GitHubVariant.DOTCOM,
@@ -777,6 +801,7 @@ for (const date of ["20200101", "30260213"]) {
             url,
             SAMPLE_DEFAULT_CLI_VERSION,
             ["java"],
+            undefined, // otherLanguagePacksReason
             false,
             SAMPLE_DOTCOM_API_DETAILS,
             GitHubVariant.DOTCOM,
@@ -804,6 +829,7 @@ for (const date of ["20200101", "30260213"]) {
               GitHubVariant.DOTCOM,
               SAMPLE_DEFAULT_CLI_VERSION,
               ["java"],
+              undefined, // otherLanguagePacksReason
               false,
               features,
               logger,
@@ -834,6 +860,7 @@ test.serial(
           "toolcache",
           SAMPLE_DEFAULT_CLI_VERSION,
           ["java"],
+          undefined, // otherLanguagePacksReason
           false,
           SAMPLE_DOTCOM_API_DETAILS,
           GitHubVariant.DOTCOM,
@@ -875,6 +902,7 @@ test.serial(
         "toolcache",
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -944,6 +972,7 @@ const toolcacheInputFallbackMacro = makeMacro({
         "toolcache",
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -1081,6 +1110,7 @@ test.serial(
         undefined,
         overlayMatchEnabledVersions,
         ["javascript"],
+        undefined, // otherLanguagePacksReason
         true,
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -1119,6 +1149,7 @@ test.serial(
         undefined,
         overlayMatchEnabledVersions,
         ["javascript"],
+        undefined, // otherLanguagePacksReason
         false,
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -1156,6 +1187,7 @@ test.serial(
         undefined,
         PER_LANGUAGE_CLI_VERSION,
         ["java-kotlin"],
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         SAMPLE_DOTCOM_API_DETAILS,
         GitHubVariant.DOTCOM,
@@ -1185,7 +1217,7 @@ test.serial(
 );
 
 test.serial(
-  "getCodeQLSource downloads the combined bundle when the feature is disabled",
+  "getCodeQLSource downloads the combined bundle when per-language selection is ineligible",
   async (t) => {
     sinon.stub(process, "platform").value("linux");
     sinon.stub(process, "arch").value("x64");
@@ -1193,22 +1225,33 @@ test.serial(
 
     await withTmpDir(async (tmpDir) => {
       setupActionsVars(tmpDir, tmpDir);
-      const source = await setupCodeql.getCodeQLSource(
-        undefined,
-        PER_LANGUAGE_CLI_VERSION,
-        ["java"],
-        false, // useOverlayAwareDefaultCliVersion
-        SAMPLE_DOTCOM_API_DETAILS,
-        GitHubVariant.DOTCOM,
-        true, // tarSupportsZstd
-        createFeatures([]),
-        getRunnerLogger(true),
-      );
+      for (const { otherLanguagePacksReason, features } of [
+        // The per-language feature is disabled.
+        { otherLanguagePacksReason: undefined, features: createFeatures([]) },
+        // The configured queries may need library packs for other languages.
+        {
+          otherLanguagePacksReason: "an example reason",
+          features: createFeatures([Feature.PerLanguageBundles]),
+        },
+      ]) {
+        const source = await setupCodeql.getCodeQLSource(
+          undefined,
+          PER_LANGUAGE_CLI_VERSION,
+          ["java"],
+          otherLanguagePacksReason,
+          false, // useOverlayAwareDefaultCliVersion
+          SAMPLE_DOTCOM_API_DETAILS,
+          GitHubVariant.DOTCOM,
+          true, // tarSupportsZstd
+          features,
+          getRunnerLogger(true),
+        );
 
-      t.is(source.sourceType, "download");
-      if (source.sourceType === "download") {
-        t.true(source.bundle.url.endsWith("/codeql-bundle-linux64.tar.zst"));
-        t.is(source.bundle.kind, "combined");
+        t.is(source.sourceType, "download");
+        if (source.sourceType === "download") {
+          t.true(source.bundle.url.endsWith("/codeql-bundle-linux64.tar.zst"));
+          t.is(source.bundle.kind, "combined");
+        }
       }
     });
   },
@@ -1268,6 +1311,7 @@ for (const fallback of [false, true]) {
           GitHubVariant.DOTCOM,
           PER_LANGUAGE_CLI_VERSION,
           ["java"],
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           createFeatures([Feature.PerLanguageBundles]),
           getRunnerLogger(true),
@@ -1363,6 +1407,7 @@ for (const bundle of ["per-language", "combined", "fallback"] as const) {
           GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           bundle === "combined" ? ["javascript", "python"] : ["javascript"],
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           features,
           logger,
@@ -1443,6 +1488,7 @@ for (const bundle of ["per-language", "combined", "fallback"] as const) {
             GitHubVariant.DOTCOM,
             SAMPLE_DEFAULT_CLI_VERSION,
             ["javascript"],
+            undefined, // otherLanguagePacksReason
             false, // useOverlayAwareDefaultCliVersion
             features,
             logger,
@@ -1478,6 +1524,7 @@ for (const asset of [
           GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           createFeatures([]),
           getRecordingLogger(messages),
@@ -1532,6 +1579,7 @@ for (const error of [
             GitHubVariant.DOTCOM,
             PER_LANGUAGE_CLI_VERSION,
             ["java"],
+            undefined, // otherLanguagePacksReason
             false, // useOverlayAwareDefaultCliVersion
             createFeatures([Feature.PerLanguageBundles]),
             getRunnerLogger(true),
@@ -1567,6 +1615,7 @@ test.serial(
           GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           createFeatures([]),
           getRunnerLogger(true),
@@ -2239,6 +2288,7 @@ test.serial(
         GitHubVariant.DOTCOM,
         SAMPLE_DEFAULT_CLI_VERSION,
         undefined, // rawLanguages
+        undefined, // otherLanguagePacksReason
         false, // useOverlayAwareDefaultCliVersion
         createFeatures([]),
         getRunnerLogger(true),
@@ -2278,6 +2328,7 @@ test.serial(
           GitHubVariant.DOTCOM,
           SAMPLE_DEFAULT_CLI_VERSION,
           undefined, // rawLanguages
+          undefined, // otherLanguagePacksReason
           false, // useOverlayAwareDefaultCliVersion
           createFeatures([Feature.CleanupToolcacheBundles]),
           getRunnerLogger(true),
diff --git a/src/setup-codeql.ts b/src/setup-codeql.ts
index d306d40d63..f2ce959a8d 100644
--- a/src/setup-codeql.ts
+++ b/src/setup-codeql.ts
@@ -377,6 +377,9 @@ async function resolveDefaultCliVersion(
  * @param toolsInput The argument provided for the `tools` input, if any.
  * @param defaultCliVersion The default CLI version that's linked to the CodeQL Action.
  * @param rawLanguages Raw set of languages.
+ * @param otherLanguagePacksReason Why the CodeQL CLI may need packs for languages other than
+ *   `rawLanguages`, or `undefined` if it won't. If defined, the combined bundle is used. See
+ *   `PerLanguageBundleOptions.otherLanguagePacksReason`.
  * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
  * @param apiDetails Information about the GitHub API.
  * @param variant The GitHub variant we are running on.
@@ -390,6 +393,7 @@ export async function getCodeQLSource(
   toolsInput: string | undefined,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
   useOverlayAwareDefaultCliVersion: boolean,
   apiDetails: api.GitHubApiDetails,
   variant: util.GitHubVariant,
@@ -478,6 +482,7 @@ export async function getCodeQLSource(
     bundle = await getLatestNightlyBundle(
       { env: getEnv(), features, logger },
       rawLanguages,
+      otherLanguagePacksReason,
       variant,
     );
     toolsInput = bundle.url;
@@ -721,6 +726,7 @@ export async function getCodeQLSource(
       { env: getEnv(), features, logger },
       {
         rawLanguages,
+        otherLanguagePacksReason,
         cliVersion,
         compressionMethod,
         platform,
@@ -1001,6 +1007,7 @@ export async function setupCodeQLBundle(
   variant: util.GitHubVariant,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
   useOverlayAwareDefaultCliVersion: boolean,
   features: FeatureEnablement,
   logger: Logger,
@@ -1016,6 +1023,7 @@ export async function setupCodeQLBundle(
     toolsInput,
     defaultCliVersion,
     rawLanguages,
+    otherLanguagePacksReason,
     useOverlayAwareDefaultCliVersion,
     apiDetails,
     variant,
@@ -1159,6 +1167,7 @@ function getTempExtractionDir(tempDir: string) {
 async function getLatestNightlyBundle(
   action: ActionState<["Logger", "ReadOnlyEnv", "FeatureFlags"]>,
   rawLanguages: string[] | undefined,
+  otherLanguagePacksReason: string | undefined,
   variant: util.GitHubVariant,
 ): Promise<CodeQLBundle> {
   const { logger } = action;
@@ -1174,6 +1183,7 @@ async function getLatestNightlyBundle(
   const platform = getBundlePlatform();
   const language = await getPerLanguageBundleLanguage(action, {
     rawLanguages,
+    otherLanguagePacksReason,
     cliVersion: undefined,
     compressionMethod,
     platform,
diff --git a/src/upload-lib.ts b/src/upload-lib.ts
index da5552cf24..c5b6c6efd5 100644
--- a/src/upload-lib.ts
+++ b/src/upload-lib.ts
@@ -166,6 +166,7 @@ async function combineSarifFilesUsingCLI(
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       undefined, // rawLanguages: upload-lib does not run analysis
+      undefined, // otherLanguagePacksReason: upload-lib does not run analysis
       false, // useOverlayAwareDefaultCliVersion: upload-lib does not run analysis
       features,
       logger,