diff --git a/packages/amplify-e2e-core/src/categories/hosting.ts b/packages/amplify-e2e-core/src/categories/hosting.ts
index cc7b13c5ec2..bea05eefecc 100644
--- a/packages/amplify-e2e-core/src/categories/hosting.ts
+++ b/packages/amplify-e2e-core/src/categories/hosting.ts
@@ -129,6 +129,21 @@ export function amplifyPushWithUpdate(cwd: string): Promise<void> {
   });
 }
 
+export function amplifyPublishWithUpdate(cwd: string): Promise<void> {
+  return new Promise((resolve, reject) => {
+    spawn(getCLIPath(), ['publish'], { cwd, stripColors: true })
+      .wait('Are you sure you want to continue?')
+      .sendCarriageReturn()
+      .run((err: Error) => {
+        if (!err) {
+          resolve();
+        } else {
+          reject(err);
+        }
+      });
+  });
+}
+
 export function amplifyPublishWithoutUpdate(cwd: string): Promise<void> {
   return new Promise((resolve, reject) => {
     spawn(getCLIPath(), ['publish'], { cwd, stripColors: true }).run((err: Error) => {
diff --git a/packages/amplify-e2e-tests/src/__tests__/hostingPROD.test.ts b/packages/amplify-e2e-tests/src/__tests__/hostingPROD.test.ts
index a090e62d245..1824a422509 100644
--- a/packages/amplify-e2e-tests/src/__tests__/hostingPROD.test.ts
+++ b/packages/amplify-e2e-tests/src/__tests__/hostingPROD.test.ts
@@ -1,5 +1,5 @@
 import { CloudFront } from 'aws-sdk';
-import { amplifyPublishWithoutUpdate, createReactTestProject, resetBuildCommand } from 'amplify-e2e-core';
+import { amplifyPublishWithoutUpdate, amplifyPublishWithUpdate, createReactTestProject, resetBuildCommand } from 'amplify-e2e-core';
 
 import { initJSProjectWithProfile, deleteProject, deleteS3Bucket } from 'amplify-e2e-core';
 import { addPRODHosting, removePRODCloudFront, removeHosting, amplifyPushWithoutCodegen } from 'amplify-e2e-core';
@@ -45,7 +45,8 @@ describe('amplify add hosting', () => {
   it('publish successfully', async () => {
     let error;
     try {
-      await amplifyPublishWithoutUpdate(projRoot);
+      // root stack updated
+      await amplifyPublishWithUpdate(projRoot);
     } catch (err) {
       error = err;
     }
@@ -56,7 +57,7 @@ describe('amplify add hosting', () => {
     const currentBuildCommand = resetBuildCommand(projRoot, '');
     let error;
     try {
-      await amplifyPublishWithoutUpdate(projRoot);
+      await amplifyPublishWithUpdate(projRoot);
     } catch (err) {
       error = err;
     }
diff --git a/packages/amplify-e2e-tests/src/__tests__/init.test.ts b/packages/amplify-e2e-tests/src/__tests__/init.test.ts
index 7ba2f0c16f8..b1ad904e980 100644
--- a/packages/amplify-e2e-tests/src/__tests__/init.test.ts
+++ b/packages/amplify-e2e-tests/src/__tests__/init.test.ts
@@ -29,8 +29,8 @@ describe('amplify init', () => {
   });
 
   afterEach(async () => {
-    // await deleteProject(projRoot);
-    // deleteProjectDir(projRoot);
+    await deleteProject(projRoot);
+    deleteProjectDir(projRoot);
   });
 
   it('should pull sandbox and download schema', async () => {
diff --git a/packages/amplify-provider-awscloudformation/src/initializer.ts b/packages/amplify-provider-awscloudformation/src/initializer.ts
index dcc02e4822a..11bea2b5197 100644
--- a/packages/amplify-provider-awscloudformation/src/initializer.ts
+++ b/packages/amplify-provider-awscloudformation/src/initializer.ts
@@ -183,9 +183,9 @@ export const storeRootStackTemplate = async (context: $TSContext, template?: Tem
   // generate template again as the folder structure was not created when root stack was initiaized
   if (template === undefined) {
     template = await transformRootStack(context);
-    await prePushCfnTemplateModifier(template);
   }
-
+  // apply Modifiers
+  await prePushCfnTemplateModifier(template);
   // RootStack deployed to backend/awscloudformation/build
   const projectRoot = pathManager.findProjectRoot();
   const rootStackBackendBuildDir = pathManager.getRootStackBuildDirPath(projectRoot);
diff --git a/packages/amplify-provider-awscloudformation/src/override-manager/transform-resource.ts b/packages/amplify-provider-awscloudformation/src/override-manager/transform-resource.ts
index 9f2d0e2eb4b..945800d5644 100644
--- a/packages/amplify-provider-awscloudformation/src/override-manager/transform-resource.ts
+++ b/packages/amplify-provider-awscloudformation/src/override-manager/transform-resource.ts
@@ -22,9 +22,14 @@ export async function transformResourceWithOverrides(context: $TSContext, resour
         printer.info('Overrides functionality is not impleented for this category');
       }
     } else {
-      if (FeatureFlags.getBoolean('overrides.project')) {
-        await storeRootStackTemplate(context);
-      }
+      const template = await transformRootStack(context);
+      await prePushCfnTemplateModifier(template);
+      // RootStack deployed to backend/awscloudformation/build
+      const projectRoot = pathManager.findProjectRoot();
+      const rootStackBackendBuildDir = pathManager.getRootStackBuildDirPath(projectRoot);
+      fs.ensureDirSync(rootStackBackendBuildDir);
+      const rootStackBackendFilePath = path.join(rootStackBackendBuildDir, rootStackFileName);
+      JSONUtilities.writeJson(rootStackBackendFilePath, template);
     }
   } catch (err) {
     return;