diff --git a/.changeset/devkit-scrub-git-hook-env.md b/.changeset/devkit-scrub-git-hook-env.md
new file mode 100644
index 000000000..ee7874550
--- /dev/null
+++ b/.changeset/devkit-scrub-git-hook-env.md
@@ -0,0 +1,13 @@
+---
+'@xnetjs/devkit': patch
+---
+
+`NodeCommandRunner` now scrubs git repo-location env vars (`GIT_DIR`,
+`GIT_WORK_TREE`, `GIT_INDEX_FILE`, `GIT_OBJECT_DIRECTORY`,
+`GIT_ALTERNATE_OBJECT_DIRECTORIES`, `GIT_COMMON_DIR`, `GIT_PREFIX`) from the
+inherited environment before spawning subprocesses. Previously, running devkit
+inside a git hook (where `git commit` exports `GIT_INDEX_FILE`) silently
+redirected every spawned `git` at the hook's repository instead of the caller's
+`cwd`, breaking temp-repo workflows and worktree creation with errors like
+".git/index: index file open failed: Not a directory". An explicit value passed
+via `options.env` still wins.
diff --git a/.husky/pre-commit b/.husky/pre-commit
index 64fc3e1ac..50c7e7551 100755
--- a/.husky/pre-commit
+++ b/.husky/pre-commit
@@ -119,4 +119,7 @@ fi
 
 pnpm lint-staged
 pnpm turbo run typecheck --affected
-pnpm vitest run --changed HEAD --passWithNoTests
+# Scrub the repo-location env vars `git commit` exports into hooks: tests that
+# create their own temp repos (e.g. packages/devkit) would otherwise have their
+# spawned git processes redirected at THIS repo's index and fail.
+env -u GIT_INDEX_FILE -u GIT_DIR -u GIT_WORK_TREE pnpm vitest run --changed HEAD --passWithNoTests
diff --git a/packages/devkit/src/command-runner.test.ts b/packages/devkit/src/command-runner.test.ts
index 482b0d309..b95e62a4d 100644
--- a/packages/devkit/src/command-runner.test.ts
+++ b/packages/devkit/src/command-runner.test.ts
@@ -58,4 +58,25 @@ describe('NodeCommandRunner (real subprocess)', () => {
     expect(r.ok).toBe(false)
     expect(r.code).toBe(-1)
   })
+
+  it('scrubs inherited git repo-location vars but honours explicit env overrides', async () => {
+    // Simulate running inside a git hook (`git commit` exports GIT_INDEX_FILE).
+    process.env.GIT_INDEX_FILE = '/parent/repo/.git/index'
+    process.env.GIT_DIR = '/parent/repo/.git'
+    try {
+      const print =
+        "process.stdout.write(String(process.env.GIT_INDEX_FILE ?? '') + '|' + String(process.env.GIT_DIR ?? ''))"
+      const scrubbed = await runner.run('node', ['-e', print], { cwd: process.cwd() })
+      expect(scrubbed.stdout).toBe('|')
+
+      const overridden = await runner.run('node', ['-e', print], {
+        cwd: process.cwd(),
+        env: { GIT_INDEX_FILE: '/explicit/index' }
+      })
+      expect(overridden.stdout).toBe('/explicit/index|')
+    } finally {
+      delete process.env.GIT_INDEX_FILE
+      delete process.env.GIT_DIR
+    }
+  })
 })
diff --git a/packages/devkit/src/command-runner.ts b/packages/devkit/src/command-runner.ts
index 6064552d8..45a7fed7f 100644
--- a/packages/devkit/src/command-runner.ts
+++ b/packages/devkit/src/command-runner.ts
@@ -10,6 +10,32 @@
 
 import { spawn } from 'node:child_process'
 
+/**
+ * Repo-location env vars that `git` exports into hook subprocesses (e.g.
+ * `git commit` sets GIT_INDEX_FILE for pre-commit hooks). If a devkit process
+ * runs inside a hook and inherits these, every spawned `git` is silently
+ * redirected at the hook's repo instead of the `cwd` the caller asked for —
+ * temp-repo tests and agent worktrees break with errors like
+ * ".git/index: index file open failed: Not a directory". The runner drops them
+ * from the inherited env; a caller that really wants one can still set it
+ * explicitly via `options.env`.
+ */
+const GIT_REPO_LOCATION_VARS = [
+  'GIT_DIR',
+  'GIT_WORK_TREE',
+  'GIT_INDEX_FILE',
+  'GIT_OBJECT_DIRECTORY',
+  'GIT_ALTERNATE_OBJECT_DIRECTORIES',
+  'GIT_COMMON_DIR',
+  'GIT_PREFIX'
+] as const
+
+function sanitizedEnv(): NodeJS.ProcessEnv {
+  const env = { ...process.env }
+  for (const key of GIT_REPO_LOCATION_VARS) delete env[key]
+  return env
+}
+
 export interface CommandResult {
   /** `true` when the process exited 0. */
   ok: boolean
@@ -40,7 +66,7 @@ export class NodeCommandRunner implements CommandRunner {
     return new Promise((resolve) => {
       const child = spawn(command, args, {
         cwd: options.cwd,
-        env: { ...process.env, ...options.env },
+        env: { ...sanitizedEnv(), ...options.env },
         shell: false // never interpret the command through a shell
       })
       let stdout = ''