diff --git a/packages/rstack/src/setup/install.ts b/packages/rstack/src/setup/install.ts
index bd0bb407..ad900faf 100644
--- a/packages/rstack/src/setup/install.ts
+++ b/packages/rstack/src/setup/install.ts
@@ -7,6 +7,7 @@ import {
   writeFileSync,
 } from 'node:fs';
 import path from 'node:path';
+import { types } from 'node:util';
 import {
   displayPath,
   fail,
@@ -156,7 +157,7 @@ const claimOwner = (
     writeFileSync(ownerPath, `${project}\n`, { flag: 'wx' });
   } catch (error) {
     const code =
-      error instanceof Error && 'code' in error ? error.code : undefined;
+      types.isNativeError(error) && 'code' in error ? error.code : undefined;
     if (code !== 'EEXIST') {
       throw error;
     }
@@ -285,7 +286,7 @@ export const installHooks = ({
       chmodSync(filePath, 0o755);
     }
   } catch (error) {
-    const message = error instanceof Error ? error.message : String(error);
+    const message = types.isNativeError(error) ? error.message : String(error);
     return fail('write-failed', `Failed to write Git hook files: ${message}`);
   }
 
diff --git a/packages/rstack/tests/setup/install-errors.test.ts b/packages/rstack/tests/setup/install-errors.test.ts
new file mode 100644
index 00000000..7733a4a1
--- /dev/null
+++ b/packages/rstack/tests/setup/install-errors.test.ts
@@ -0,0 +1,54 @@
+import { existsSync, writeFileSync } from 'node:fs';
+import path from 'node:path';
+import { runInNewContext } from 'node:vm';
+import { afterEach, expect, rs, test } from 'rstack/test';
+import { installHooks } from '../../src/setup/install.ts';
+import { git, hooksPath, withRepository } from './helpers.ts';
+
+rs.mock('node:fs', () => {
+  const actual = rs.requireActual<typeof import('node:fs')>('node:fs');
+  return { ...actual, writeFileSync: rs.fn(actual.writeFileSync) };
+});
+
+afterEach(() => {
+  rs.mocked(writeFileSync).mockReset();
+});
+
+test('handles cross-realm owner file conflicts', () => {
+  withRepository((cwd) => {
+    const error: unknown = runInNewContext(
+      'Object.assign(new Error("owner file exists"), { code: "EEXIST" })',
+    );
+    expect(error instanceof Error).toBe(false);
+    rs.mocked(writeFileSync).mockImplementationOnce(() => {
+      throw error;
+    });
+
+    expect(installHooks({ cwd })).toMatchObject({
+      status: 'skipped',
+      reason: 'hooks-directory-conflict',
+    });
+    expect(existsSync(path.join(cwd, hooksPath, 'runner'))).toBe(false);
+    expect(
+      git(cwd, ['config', '--local', '--get', 'core.hooksPath']).status,
+    ).toBe(1);
+  });
+});
+
+test('preserves the message of cross-realm filesystem errors', () => {
+  withRepository((cwd) => {
+    const error: unknown = runInNewContext(
+      'Object.assign(new Error("permission denied"), { code: "EACCES" })',
+    );
+    expect(error instanceof Error).toBe(false);
+    rs.mocked(writeFileSync).mockImplementationOnce(() => {
+      throw error;
+    });
+
+    expect(installHooks({ cwd })).toEqual({
+      status: 'failed',
+      reason: 'write-failed',
+      message: 'Failed to write Git hook files: permission denied',
+    });
+  });
+});