diff --git a/common/changes/@microsoft/rush/fix-git-dir-worktree-hook-repo-root_2026-06-08-19-02.json b/common/changes/@microsoft/rush/fix-git-dir-worktree-hook-repo-root_2026-06-08-19-02.json
new file mode 100644
index 0000000000..1c9c893417
--- /dev/null
+++ b/common/changes/@microsoft/rush/fix-git-dir-worktree-hook-repo-root_2026-06-08-19-02.json
@@ -0,0 +1,10 @@
+{
+  "changes": [
+    {
+      "packageName": "@microsoft/rush",
+      "comment": "Fix build cache failures when running inside a git linked worktree via a pre-commit hook, caused by GIT_DIR being set to the per-worktree metadata directory",
+      "type": "none"
+    }
+  ],
+  "packageName": "@microsoft/rush"
+}
\ No newline at end of file
diff --git a/common/changes/@rushstack/package-deps-hash/fix-git-dir-worktree-hook_2026-06-03-00-00.json b/common/changes/@rushstack/package-deps-hash/fix-git-dir-worktree-hook_2026-06-03-00-00.json
new file mode 100644
index 0000000000..d67ccffa27
--- /dev/null
+++ b/common/changes/@rushstack/package-deps-hash/fix-git-dir-worktree-hook_2026-06-03-00-00.json
@@ -0,0 +1,11 @@
+{
+  "changes": [
+    {
+      "comment": "Strip GIT_DIR and GIT_WORK_TREE Node env variables to fix issues with miscalculating the git repo root when working in a linked worktree",
+      "type": "patch",
+      "packageName": "@rushstack/package-deps-hash"
+    }
+  ],
+  "packageName": "@rushstack/package-deps-hash",
+  "email": "istateside@users.noreply.github.com"
+}
diff --git a/libraries/package-deps-hash/src/getRepoState.ts b/libraries/package-deps-hash/src/getRepoState.ts
index 7f01cde162..45cb07a8dd 100644
--- a/libraries/package-deps-hash/src/getRepoState.ts
+++ b/libraries/package-deps-hash/src/getRepoState.ts
@@ -33,9 +33,28 @@ const STANDARD_GIT_OPTIONS: readonly string[] = [
 // `git hash-object` aborts the process. Such files are typically untracked artifacts left behind
 // by tooling (e.g. stray `nul` from a shell redirect).
 const WINDOWS_RESERVED_BASENAMES: ReadonlySet<string> = new Set([
-  'CON', 'PRN', 'AUX', 'NUL',
-  'COM1', 'COM2', 'COM3', 'COM4', 'COM5', 'COM6', 'COM7', 'COM8', 'COM9',
-  'LPT1', 'LPT2', 'LPT3', 'LPT4', 'LPT5', 'LPT6', 'LPT7', 'LPT8', 'LPT9'
+  'CON',
+  'PRN',
+  'AUX',
+  'NUL',
+  'COM1',
+  'COM2',
+  'COM3',
+  'COM4',
+  'COM5',
+  'COM6',
+  'COM7',
+  'COM8',
+  'COM9',
+  'LPT1',
+  'LPT2',
+  'LPT3',
+  'LPT4',
+  'LPT5',
+  'LPT6',
+  'LPT7',
+  'LPT8',
+  'LPT9'
 ]);
 
 /**
@@ -254,6 +273,13 @@ export function parseGitStatus(output: string): Map<string, boolean> {
 
 const repoRootCache: Map<string, string> = new Map();
 
+// Strip GIT_DIR/GIT_WORK_TREE: git hooks in linked worktrees set GIT_DIR to the per-worktree metadata dir, causing rev-parse --show-toplevel to return CWD instead of the worktree root.
+function getCleanGitEnvironment(): NodeJS.ProcessEnv {
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  const { GIT_DIR, GIT_WORK_TREE, ...trimmedEnv } = process.env;
+  return trimmedEnv;
+}
+
 /**
  * Finds the root of the current Git repository
  *
@@ -270,7 +296,8 @@ export function getRepoRoot(currentWorkingDirectory: string, gitPath?: string):
       gitPath || 'git',
       ['--no-optional-locks', 'rev-parse', '--show-toplevel'],
       {
-        currentWorkingDirectory
+        currentWorkingDirectory,
+        environment: getCleanGitEnvironment()
       }
     );
 
@@ -305,7 +332,8 @@ async function spawnGitAsync(
 ): Promise<string> {
   const spawnOptions: IExecutableSpawnOptions = {
     currentWorkingDirectory,
-    stdio: ['pipe', 'pipe', 'pipe']
+    stdio: ['pipe', 'pipe', 'pipe'],
+    environment: getCleanGitEnvironment()
   };
 
   let stdout: string = '';
@@ -591,7 +619,8 @@ export function getRepoChanges(
       '--'
     ]),
     {
-      currentWorkingDirectory: rootDirectory
+      currentWorkingDirectory: rootDirectory,
+      environment: getCleanGitEnvironment()
     }
   );
 
diff --git a/libraries/package-deps-hash/src/test/getRepoDeps.test.ts b/libraries/package-deps-hash/src/test/getRepoDeps.test.ts
index 6e01af1fd6..c78e034386 100644
--- a/libraries/package-deps-hash/src/test/getRepoDeps.test.ts
+++ b/libraries/package-deps-hash/src/test/getRepoDeps.test.ts
@@ -2,7 +2,7 @@
 // See LICENSE in the project root for license information.
 
 import * as path from 'node:path';
-import { execSync } from 'node:child_process';
+import { execSync, type SpawnSyncReturns } from 'node:child_process';
 
 import {
   getDetailedRepoStateAsync,
@@ -12,7 +12,7 @@ import {
   parseGitHashObject
 } from '../getRepoState';
 
-import { FileSystem } from '@rushstack/node-core-library';
+import { Executable, FileSystem } from '@rushstack/node-core-library';
 
 const SOURCE_PATH: string = path
   .join(__dirname)
@@ -45,6 +45,59 @@ describe(getRepoRoot.name, () => {
     const expectedRoot: string = path.resolve(__dirname, '../../../..').replace(/\\/g, '/');
     expect(root).toEqual(expectedRoot);
   });
+
+  it(`strips GIT_DIR and GIT_WORK_TREE before invoking git`, () => {
+    // Regression test for the linked-worktree bug. When git runs a hook it injects GIT_DIR (and
+    // sometimes GIT_WORK_TREE) into the environment; in a linked worktree GIT_DIR points at the
+    // per-worktree metadata directory, which makes `git rev-parse --show-toplevel` resolve against
+    // the current directory instead of the true repository root. getRepoRoot must therefore invoke
+    // git with those variables removed, so the root is derived solely from currentWorkingDirectory.
+    //
+    // This is asserted at the spawn boundary rather than by mutating process.env and shelling out for
+    // real: the Jest environment does not propagate in-process process.env writes to child processes,
+    // so an end-to-end variant would pass whether or not the stripping actually happens.
+    const fakeRoot: string = '/fake/repo/root';
+    const mockResult: SpawnSyncReturns<string> = {
+      pid: 0,
+      output: [],
+      stdout: fakeRoot,
+      stderr: '',
+      status: 0,
+      signal: null
+    };
+    const spawnSyncSpy: jest.SpyInstance = jest.spyOn(Executable, 'spawnSync').mockReturnValue(mockResult);
+
+    const originalGitDir: string | undefined = process.env.GIT_DIR;
+    const originalGitWorkTree: string | undefined = process.env.GIT_WORK_TREE;
+    try {
+      process.env.GIT_DIR = '/repo/.git/worktrees/feature';
+      process.env.GIT_WORK_TREE = '/repo/work/tree';
+
+      // A unique cwd that no other test resolves, so getRepoRoot's module-level cache can't satisfy
+      // this from a previous call and skip the spawn.
+      getRepoRoot('/nonexistent/getRepoRoot-strips-git-env');
+
+      expect(spawnSyncSpy).toHaveBeenCalledTimes(1);
+      const passedEnvironment: NodeJS.ProcessEnv | undefined = spawnSyncSpy.mock.calls[0][2]?.environment;
+      // The fix passes an explicit environment (pre-fix code passed none) that omits both variables,
+      // while leaving the rest of process.env intact.
+      expect(passedEnvironment).toBeDefined();
+      expect(passedEnvironment).not.toHaveProperty('GIT_DIR');
+      expect(passedEnvironment).not.toHaveProperty('GIT_WORK_TREE');
+    } finally {
+      spawnSyncSpy.mockRestore();
+      if (originalGitDir === undefined) {
+        delete process.env.GIT_DIR;
+      } else {
+        process.env.GIT_DIR = originalGitDir;
+      }
+      if (originalGitWorkTree === undefined) {
+        delete process.env.GIT_WORK_TREE;
+      } else {
+        process.env.GIT_WORK_TREE = originalGitWorkTree;
+      }
+    }
+  });
 });
 
 describe(parseGitLsTree.name, () => {