diff --git a/packages/amplify-e2e-tests/src/__tests__/hooks-a.test.ts b/packages/amplify-e2e-tests/src/__tests__/hooks-a.test.ts
new file mode 100644
index 00000000000..f21b3e351d8
--- /dev/null
+++ b/packages/amplify-e2e-tests/src/__tests__/hooks-a.test.ts
@@ -0,0 +1,37 @@
+import {
+  addFunction, amplifyPullNonInteractive, amplifyPushAuth, createNewProjectDir,
+  deleteProject,
+  deleteProjectDir,
+  getBackendAmplifyMeta, getHooksDirPath, initJSProjectWithProfile, transformCurrentProjectToGitPulledProject,
+} from '@aws-amplify/amplify-e2e-core';
+import * as fs from 'fs-extra';
+import * as path from 'path';
+
+describe('runtime hooks', () => {
+  let projRoot: string;
+  beforeEach(async () => {
+    projRoot = await createNewProjectDir('hooks');
+  });
+
+  afterEach(async () => {
+    await deleteProject(projRoot);
+    deleteProjectDir(projRoot);
+  });
+
+  it('hooks should not get deleted when pulling a project from git and running amplify pull', async () => {
+    await initJSProjectWithProfile(projRoot, { envName: 'staging', disableAmplifyAppCreation: false });
+    const appId = getBackendAmplifyMeta(projRoot)?.providers?.awscloudformation?.AmplifyAppId;
+    expect(appId).toBeDefined();
+    const hooksDirPath = getHooksDirPath(projRoot);
+    expect(fs.existsSync(hooksDirPath)).toBe(true);
+    fs.removeSync(path.join(hooksDirPath, 'pre-push.js.sample'));
+    fs.removeSync(path.join(hooksDirPath, 'post-push.sh.sample'));
+    fs.writeFileSync(path.join(hooksDirPath, 'pre-push.js'), `console.log('hello');`);
+    await addFunction(projRoot, { functionTemplate: 'Hello World' }, 'nodejs');
+    await amplifyPushAuth(projRoot);
+    // grab the appId from the meta file
+    transformCurrentProjectToGitPulledProject(projRoot);
+    await amplifyPullNonInteractive(projRoot, { appId, envName: 'staging' });
+    expect(fs.existsSync(hooksDirPath)).toBe(true);
+  });
+});
diff --git a/packages/amplify-e2e-tests/src/__tests__/hooks-b.test.ts b/packages/amplify-e2e-tests/src/__tests__/hooks-b.test.ts
new file mode 100644
index 00000000000..bb085d4ef85
--- /dev/null
+++ b/packages/amplify-e2e-tests/src/__tests__/hooks-b.test.ts
@@ -0,0 +1,34 @@
+import {
+  addFunction, createNewProjectDir,
+  deleteProject,
+  deleteProjectDir, getHooksDirPath, initJSProjectWithProfile,
+} from '@aws-amplify/amplify-e2e-core';
+import * as fs from 'fs-extra';
+import * as path from 'path';
+
+describe('runtime hooks', () => {
+  let projRoot: string;
+  beforeEach(async () => {
+    projRoot = await createNewProjectDir('hooks');
+  });
+
+  afterEach(async () => {
+    await deleteProject(projRoot);
+    deleteProjectDir(projRoot);
+  });
+
+  it('test hook scripts with non zero exit code', async () => {
+    // eslint-disable-next-line spellcheck/spell-checker
+    await initJSProjectWithProfile(projRoot, { envName: 'enva' });
+    const hooksDirPath = getHooksDirPath(projRoot);
+    expect(fs.existsSync(hooksDirPath)).toBe(true);
+    fs.removeSync(path.join(hooksDirPath, 'pre-push.js.sample'));
+    fs.removeSync(path.join(hooksDirPath, 'post-push.sh.sample'));
+    fs.writeFileSync(path.join(hooksDirPath, 'pre-add.js'), 'process.exit(1);');
+
+    // amplify process should exit as the hook script exited with non zero exit code
+    await expect(addFunction(projRoot, { functionTemplate: 'Hello World' }, 'nodejs')).rejects.toThrow();
+    // expect function to be not created
+    expect(fs.readdirSync(path.join(projRoot, 'amplify', 'backend'))).not.toContain('function');
+  });
+});
diff --git a/scripts/split-e2e-tests.ts b/scripts/split-e2e-tests.ts
index 736dcd026a5..dbeaf9bb4ee 100644
--- a/scripts/split-e2e-tests.ts
+++ b/scripts/split-e2e-tests.ts
@@ -35,7 +35,7 @@ const WINDOWS_TEST_ALLOWLIST: string[] = [
   'schema-auth-11-c_pkg',
   'auth_6_pkg',
   'frontend_config_drift_pkg',
-  'hooks_pkg',
+  'hooks-b_pkg',
   'plugin_pkg',
   'schema-versioned_pkg',
   'schema-auth-3_pkg',