diff --git a/CHANGELOG.md b/CHANGELOG.md
index 351a3cf58..980579a20 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
+## [Unreleased]
+
+### Fixed
+- `socket fix` pull requests now include every file a fix changes, such as `package.json` override bumps, and work when run from a subdirectory of the repository.
+
 ## [1.4.0](https://github.com/SocketDev/socket-cli/releases/tag/v1.4.0) - 2026-09-29
 
 ### Changed
diff --git a/src/commands/fix/coana-fix-dynamic-sbom-inference.test.mts b/src/commands/fix/coana-fix-dynamic-sbom-inference.test.mts
index 09fe55e02..7a5fddbae 100644
--- a/src/commands/fix/coana-fix-dynamic-sbom-inference.test.mts
+++ b/src/commands/fix/coana-fix-dynamic-sbom-inference.test.mts
@@ -232,7 +232,7 @@ describe('socket fix --dynamic-sbom-inference', () => {
       })
       mockGitUnstagedModifiedFiles.mockResolvedValue({
         ok: true,
-        data: ['app/build.gradle', 'gradle/versions.gradle', 'README.md'],
+        data: ['app/build.gradle', 'gradle/versions.gradle'],
       })
 
       await coanaFix({ ...baseConfig, ghsas: ['GHSA-1111-1111-1111'] })
diff --git a/src/commands/fix/coana-fix-pr-files.test.mts b/src/commands/fix/coana-fix-pr-files.test.mts
new file mode 100644
index 000000000..633610469
--- /dev/null
+++ b/src/commands/fix/coana-fix-pr-files.test.mts
@@ -0,0 +1,241 @@
+import { promises as fs } from 'node:fs'
+
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+
+import { coanaFix } from './coana-fix.mts'
+
+import type { FixConfig } from './types.mts'
+
+const mockSpawnCoanaDlx = vi.hoisted(() => vi.fn())
+const mockSetupSdk = vi.hoisted(() => vi.fn())
+const mockFetchSupportedScanFileNames = vi.hoisted(() => vi.fn())
+const mockGetPackageFilesForScan = vi.hoisted(() => vi.fn())
+const mockHandleApiCall = vi.hoisted(() => vi.fn())
+const mockGetFixEnv = vi.hoisted(() => vi.fn())
+const mockGetSocketFixPrs = vi.hoisted(() => vi.fn())
+const mockFetchGhsaDetails = vi.hoisted(() => vi.fn())
+const mockGitUnstagedModifiedFiles = vi.hoisted(() => vi.fn())
+const mockGitUntrackedFiles = vi.hoisted(() => vi.fn())
+const mockGitCommit = vi.hoisted(() => vi.fn())
+
+vi.mock('../../utils/dlx.mts', () => ({
+  spawnCoanaDlx: mockSpawnCoanaDlx,
+}))
+
+vi.mock('../../utils/sdk.mts', () => ({
+  setupSdk: mockSetupSdk,
+}))
+
+vi.mock('../scan/fetch-supported-scan-file-names.mts', () => ({
+  fetchSupportedScanFileNames: mockFetchSupportedScanFileNames,
+}))
+
+vi.mock('../../utils/path-resolve.mts', () => ({
+  getPackageFilesForScan: mockGetPackageFilesForScan,
+}))
+
+vi.mock('../../utils/api.mts', () => ({
+  handleApiCall: mockHandleApiCall,
+}))
+
+vi.mock('./env-helpers.mts', () => ({
+  checkCiEnvVars: vi.fn(() => ({ missing: [], present: [] })),
+  getCiEnvInstructions: vi.fn(() => 'Set CI env vars'),
+  getFixEnv: mockGetFixEnv,
+}))
+
+vi.mock('./pull-request.mts', () => ({
+  getSocketFixPrs: mockGetSocketFixPrs,
+  openSocketFixPr: vi.fn(async () => ({ ok: false, error: new Error('') })),
+}))
+
+vi.mock('../../utils/github.mts', () => ({
+  enablePrAutoMerge: vi.fn(),
+  fetchGhsaDetails: mockFetchGhsaDetails,
+  setGitRemoteGithubRepoUrl: vi.fn(),
+}))
+
+vi.mock('../../utils/git.mts', () => ({
+  gitCheckoutBranch: vi.fn(() => Promise.resolve(true)),
+  gitCommit: mockGitCommit,
+  gitCreateBranch: vi.fn(() => Promise.resolve(true)),
+  gitDeleteBranch: vi.fn(() => Promise.resolve(true)),
+  gitPushBranch: vi.fn(() => Promise.resolve(true)),
+  gitRemoteBranchExists: vi.fn(() => Promise.resolve(false)),
+  gitResetAndClean: vi.fn(() => Promise.resolve(true)),
+  gitUnstagedModifiedFiles: mockGitUnstagedModifiedFiles,
+  gitUntrackedFiles: mockGitUntrackedFiles,
+}))
+
+vi.mock('./branch-cleanup.mts', () => ({
+  cleanupErrorBranches: vi.fn(),
+  cleanupFailedPrBranches: vi.fn(),
+  cleanupStaleBranch: vi.fn(() => Promise.resolve(true)),
+  cleanupSuccessfulPrLocalBranch: vi.fn(),
+}))
+
+type Worktree = { modified: string[]; untracked: string[] }
+
+function committedFiles(): string[] {
+  expect(mockGitCommit).toHaveBeenCalledTimes(1)
+  return mockGitCommit.mock.calls[0]![1] as string[]
+}
+
+describe('socket fix PR mode commits', () => {
+  const baseConfig: FixConfig = {
+    all: false,
+    applyFixes: true,
+    autopilot: false,
+    coanaVersion: undefined,
+    cwd: '/test/cwd',
+    debug: false,
+    disableExternalToolChecks: false,
+    disableMajorUpdates: false,
+    ecosystems: [],
+    exclude: [],
+    excludePaths: [],
+    ghsas: ['GHSA-f8q6-p94x-37v3'],
+    include: [],
+    minSatisfying: false,
+    minimumReleaseAge: '',
+    orgSlug: 'test-org',
+    outputFile: '',
+    packageManagers: [],
+    prCheck: true,
+    prLimit: 10,
+    rangeStyle: 'preserve',
+    showAffectedDirectDependencies: false,
+    silence: true,
+    spinner: undefined,
+    unknownFlags: [],
+  }
+
+  let worktree: Worktree
+
+  function applyFix(
+    changes: Worktree,
+    modifiedFiles: string[] | undefined,
+  ): void {
+    mockSpawnCoanaDlx.mockImplementation(async (args: string[]) => {
+      worktree = {
+        modified: [...new Set([...worktree.modified, ...changes.modified])],
+        untracked: [...new Set([...worktree.untracked, ...changes.untracked])],
+      }
+      await fs.writeFile(
+        args[args.indexOf('--output-file') + 1]!,
+        JSON.stringify({ type: 'applied-fixes', fixes: {}, modifiedFiles }),
+      )
+      return { ok: true, data: '' }
+    })
+  }
+
+  beforeEach(() => {
+    vi.clearAllMocks()
+    worktree = { modified: [], untracked: [] }
+    mockSetupSdk.mockResolvedValue({
+      ok: true,
+      data: { uploadManifestFiles: vi.fn() },
+    })
+    mockFetchSupportedScanFileNames.mockResolvedValue({ ok: true, data: {} })
+    mockGetPackageFilesForScan.mockResolvedValue([
+      '/test/cwd/package.json',
+      '/test/cwd/package-lock.json',
+      '/test/cwd/pnpm-lock.yaml',
+    ])
+    mockHandleApiCall.mockResolvedValue({ ok: true, data: { tarHash: 'hash' } })
+    mockGetFixEnv.mockResolvedValue({
+      baseBranch: 'main',
+      githubToken: 'test-token',
+      gitEmail: 'test@example.com',
+      gitUser: 'test-user',
+      isCi: true,
+      repoInfo: { defaultBranch: 'main', owner: 'o', repo: 'r' },
+    })
+    mockGetSocketFixPrs.mockResolvedValue([])
+    mockFetchGhsaDetails.mockResolvedValue(new Map())
+    mockGitUnstagedModifiedFiles.mockImplementation(async () => ({
+      ok: true,
+      data: worktree.modified,
+    }))
+    mockGitUntrackedFiles.mockImplementation(async () => ({
+      ok: true,
+      data: worktree.untracked,
+    }))
+    mockGitCommit.mockResolvedValue(true)
+  })
+
+  it.each(['package-lock.json', 'pnpm-lock.yaml'])(
+    'commits a transitive override bump coana leaves out of modifiedFiles (%s)',
+    async lockfile => {
+      applyFix({ modified: ['package.json', lockfile], untracked: [] }, [
+        lockfile,
+      ])
+
+      await coanaFix(baseConfig)
+
+      expect(committedFiles()).toEqual(['package.json', lockfile])
+    },
+  )
+
+  it('commits changed tracked files when coana reports no modifiedFiles', async () => {
+    applyFix(
+      {
+        modified: ['app/build.gradle', 'gradle/versions.gradle'],
+        untracked: [],
+      },
+      undefined,
+    )
+
+    await coanaFix(baseConfig)
+
+    expect(committedFiles()).toEqual([
+      'app/build.gradle',
+      'gradle/versions.gradle',
+    ])
+  })
+
+  it('leaves out files that were dirty before the fix unless coana reports them', async () => {
+    worktree = {
+      modified: ['README.md', 'package-lock.json'],
+      untracked: ['notes.txt', 'app/.socket.facts.json'],
+    }
+    applyFix({ modified: ['package.json'], untracked: [] }, [
+      'package-lock.json',
+    ])
+
+    await coanaFix(baseConfig)
+
+    expect(committedFiles()).toEqual(['package-lock.json', 'package.json'])
+  })
+
+  it('commits new files only when coana reports them or they are manifests', async () => {
+    applyFix(
+      {
+        modified: ['build.sbt'],
+        untracked: [
+          'project/SocketDependencyOverrides.scala',
+          'sub/package-lock.json',
+          'target/classes/App.class',
+        ],
+      },
+      ['build.sbt', 'project/SocketDependencyOverrides.scala'],
+    )
+
+    await coanaFix(baseConfig)
+
+    expect(committedFiles()).toEqual([
+      'build.sbt',
+      'project/SocketDependencyOverrides.scala',
+      'sub/package-lock.json',
+    ])
+  })
+
+  it('skips the fix when it changes nothing', async () => {
+    worktree = { modified: ['package.json'], untracked: [] }
+    applyFix({ modified: [], untracked: [] }, [])
+
+    await coanaFix(baseConfig)
+
+    expect(mockGitCommit).not.toHaveBeenCalled()
+  })
+})
diff --git a/src/commands/fix/coana-fix.mts b/src/commands/fix/coana-fix.mts
index 6a7d17c3c..e76a91e33 100644
--- a/src/commands/fix/coana-fix.mts
+++ b/src/commands/fix/coana-fix.mts
@@ -198,6 +198,46 @@ function isFactsFile(filepath: string): boolean {
   return path.basename(filepath).toLowerCase() === DOT_SOCKET_DOT_FACTS_JSON
 }
 
+type GitWorkingTreeChanges = {
+  modified: string[]
+  untracked: string[]
+}
+
+async function gitWorkingTreeChanges(
+  cwd: string,
+): Promise<GitWorkingTreeChanges> {
+  const { 0: modifiedCResult, 1: untrackedCResult } = await Promise.all([
+    gitUnstagedModifiedFiles(cwd),
+    gitUntrackedFiles(cwd),
+  ])
+  return {
+    modified: modifiedCResult.ok ? modifiedCResult.data : [],
+    untracked: untrackedCResult.ok ? untrackedCResult.data : [],
+  }
+}
+
+// Coana's modifiedFiles may under-report; untracked files still need it or a
+// manifest name, so build output in repos without a .gitignore stays out.
+function selectFixedFiles(
+  before: GitWorkingTreeChanges,
+  after: GitWorkingTreeChanges,
+  writtenFiles: Set<string> | undefined,
+  scanBaseNames: Set<string>,
+): string[] {
+  const dirtyBefore = new Set([...before.modified, ...before.untracked])
+  const isFromFix = (relPath: string) =>
+    !!writtenFiles?.has(relPath) || !dirtyBefore.has(relPath)
+  return [
+    ...after.modified.filter(isFromFix),
+    ...after.untracked.filter(
+      relPath =>
+        isFromFix(relPath) &&
+        (!!writtenFiles?.has(relPath) ||
+          scanBaseNames.has(path.basename(relPath))),
+    ),
+  ]
+}
+
 function readWrittenFiles(outputFile: string): Set<string> | undefined {
   const result = readJsonSync(outputFile, { throws: false }) as
     | { modifiedFiles?: unknown }
@@ -622,6 +662,9 @@ async function coanaFixWithFacts(
     // eslint-disable-next-line no-await-in-loop
     await factsSlot?.generated?.restore()
 
+    // eslint-disable-next-line no-await-in-loop
+    const changesBefore = await gitWorkingTreeChanges(cwd)
+
     // Create a temporary file for Coana output.
     const tmpDir = os.tmpdir()
     const tmpFile = path.join(tmpDir, `socket-fix-${ghsaId}-${Date.now()}.json`)
@@ -688,24 +731,13 @@ async function coanaFixWithFacts(
       continue ghsaLoop
     }
 
-    // Check for modified files after applying the fix.
-    // eslint-disable-next-line no-await-in-loop
-    const unstagedCResult = await gitUnstagedModifiedFiles(cwd)
-    // Build scripts the fix edits need not be manifests the scan uploads,
-    // and files it creates are untracked.
-    const writtenFiles = readWrittenFiles(tmpFile)
-    // eslint-disable-next-line no-await-in-loop
-    const untrackedCResult = await gitUntrackedFiles(cwd)
-    const modifiedFiles = writtenFiles
-      ? [
-          ...(unstagedCResult.ok ? unstagedCResult.data : []),
-          ...(untrackedCResult.ok ? untrackedCResult.data : []),
-        ].filter(relPath => writtenFiles.has(relPath))
-      : unstagedCResult.ok
-        ? unstagedCResult.data.filter(relPath =>
-            scanBaseNames.has(path.basename(relPath)),
-          )
-        : []
+    const modifiedFiles = selectFixedFiles(
+      changesBefore,
+      // eslint-disable-next-line no-await-in-loop
+      await gitWorkingTreeChanges(cwd),
+      readWrittenFiles(tmpFile),
+      scanBaseNames,
+    )
 
     if (!modifiedFiles.length) {
       debugFn('notice', `skip: no changes for ${ghsaId}`)
diff --git a/src/utils/git.mts b/src/utils/git.mts
index 4d804170d..83d50552d 100644
--- a/src/utils/git.mts
+++ b/src/utils/git.mts
@@ -511,16 +511,19 @@ export async function gitUnstagedModifiedFiles(
 ): Promise<CResult<string[]>> {
   const stdioPipeOptions: SpawnOptions = { cwd }
   try {
+    // --relative matches the cwd-relative paths of `git ls-files` and
+    // `git add`; plain `git diff` prints them relative to the repo root.
     const gitDiffResult = await spawn(
       'git',
-      ['diff', '--name-only'],
+      ['diff', '--name-only', '--relative', '-z'],
       stdioPipeOptions,
     )
-    const changedFilesDetails = gitDiffResult.stdout
-    const relPaths = changedFilesDetails.split('\n')
     return {
       ok: true,
-      data: relPaths.map(p => normalizePath(p)),
+      data: gitDiffResult.stdout
+        .split('\0')
+        .filter(Boolean)
+        .map(p => normalizePath(p)),
     }
   } catch (e) {
     debugFn('error', 'Failed to get unstaged modified files')
@@ -539,13 +542,13 @@ export async function gitUntrackedFiles(
   try {
     const result = await spawn(
       'git',
-      ['ls-files', '--others', '--exclude-standard'],
+      ['ls-files', '--others', '--exclude-standard', '-z'],
       { cwd },
     )
     return {
       ok: true,
       data: result.stdout
-        .split('\n')
+        .split('\0')
         .filter(Boolean)
         .map(p => normalizePath(p)),
     }
diff --git a/src/utils/git.test.mts b/src/utils/git.test.mts
index 829475023..d4b1f83b2 100644
--- a/src/utils/git.test.mts
+++ b/src/utils/git.test.mts
@@ -1,4 +1,4 @@
-import { mkdtempSync, rmSync, writeFileSync } from 'node:fs'
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import path from 'node:path'
 
@@ -6,7 +6,13 @@ import { afterEach, beforeEach, describe, expect, it } from 'vitest'
 
 import { spawn } from '@socketsecurity/registry/lib/spawn'
 
-import { getCiBranch, gitBranch } from './git.mts'
+import {
+  getCiBranch,
+  gitBranch,
+  gitCommit,
+  gitUnstagedModifiedFiles,
+  gitUntrackedFiles,
+} from './git.mts'
 
 // GitHub Actions sets these in its own runs, so they have to be cleared for
 // the tests to exercise anything other than the CI job they run inside.
@@ -138,3 +144,61 @@ describe('gitBranch', () => {
     expect(await gitBranch(repoPath)).toBe('feature-branch')
   })
 })
+
+describe('working tree changes below the repo root', () => {
+  let repoPath = ''
+  let subPath = ''
+
+  beforeEach(async () => {
+    repoPath = await createTempRepo()
+    subPath = path.join(repoPath, 'sub')
+    mkdirSync(subPath)
+    writeFileSync(path.join(subPath, 'package.json'), '{}\n')
+    writeFileSync(path.join(repoPath, 'root.json'), '{}\n')
+    await spawn('git', ['add', '.'], { cwd: repoPath })
+    await spawn('git', ['commit', '-m', 'Add manifests'], { cwd: repoPath })
+    writeFileSync(path.join(subPath, 'package.json'), '{"a":1}\n')
+    writeFileSync(path.join(repoPath, 'root.json'), '{"a":1}\n')
+    writeFileSync(path.join(subPath, 'new file.txt'), '\n')
+  })
+
+  afterEach(() => {
+    rmSync(repoPath, { force: true, recursive: true })
+  })
+
+  it('lists modified and untracked files relative to cwd', async () => {
+    expect(await gitUnstagedModifiedFiles(subPath)).toEqual({
+      ok: true,
+      data: ['package.json'],
+    })
+    expect(await gitUntrackedFiles(subPath)).toEqual({
+      ok: true,
+      data: ['new file.txt'],
+    })
+  })
+
+  it('commits the listed paths from cwd', async () => {
+    const modified = await gitUnstagedModifiedFiles(subPath)
+    const untracked = await gitUntrackedFiles(subPath)
+    const filepaths = [
+      ...(modified.ok ? modified.data : []),
+      ...(untracked.ok ? untracked.data : []),
+    ]
+    expect(
+      await gitCommit('Fix', filepaths, {
+        cwd: subPath,
+        email: 'test@socket.dev',
+        user: 'Socket Test',
+      }),
+    ).toBe(true)
+    const committed = (
+      await spawn('git', ['show', '--name-only', '--format=', 'HEAD'], {
+        cwd: repoPath,
+      })
+    ).stdout
+    expect(committed.split('\n')).toEqual([
+      'sub/new file.txt',
+      'sub/package.json',
+    ])
+  })
+})