diff --git a/packages/amplify-cli/src/__tests__/extensions/amplify-helpers/git-manager.test.ts b/packages/amplify-cli/src/__tests__/extensions/amplify-helpers/git-manager.test.ts
index 6615bb929e5..ca489e83dbd 100644
--- a/packages/amplify-cli/src/__tests__/extensions/amplify-helpers/git-manager.test.ts
+++ b/packages/amplify-cli/src/__tests__/extensions/amplify-helpers/git-manager.test.ts
@@ -9,7 +9,9 @@ const fsMock = fs as jest.Mocked<typeof fs>;
 fsMock.readFileSync.mockImplementation(() => 'test');
 fsMock.writeFileSync.mockImplementation();
 
-const amplifyMark = '#amplify';
+const amplifyMark = '#amplify-do-not-edit-begin';
+const amplifyEndMark = '#amplify-do-not-edit-end';
+const deprecatedAmplifyMark = '#amplify';
 
 const ignoreList = [
   'amplify/\\#current-cloud-backend',
@@ -32,23 +34,38 @@ const ignoreList = [
   '.secret-*',
 ];
 
-const toAppend = `${os.EOL + os.EOL + amplifyMark + os.EOL}${ignoreList.join(os.EOL)}`;
-
+const toAppend = `${os.EOL + os.EOL + amplifyMark + os.EOL}${ignoreList.join(os.EOL)}${os.EOL + amplifyEndMark + os.EOL}`;
+const legacyToAppend = `${os.EOL + os.EOL + deprecatedAmplifyMark + os.EOL}${ignoreList.join(os.EOL)}`;
 describe('git-manager', () => {
   beforeEach(() => {
     fsMock.writeFileSync.mockClear();
+    fsMock.readFileSync.mockClear();
+    fsMock.appendFileSync.mockClear();
+    fsMock.existsSync.mockClear();
   });
   const gitIgnoreFilePath = 'testPath';
   test('appends files to an existing .gitignore', () => {
     fsMock.existsSync.mockImplementation(() => true);
+    fsMock.readFileSync.mockImplementation(() => 'amplify/');
     insertAmplifyIgnore(gitIgnoreFilePath);
-    expect(fsMock.appendFileSync.mock.calls[0][0]).toEqual('testPath');
+    expect(fsMock.writeFileSync.mock.calls[0][0]).toEqual(gitIgnoreFilePath);
+    expect(fsMock.writeFileSync.mock.calls[0][1]).toEqual('amplify/');
+    expect(fsMock.appendFileSync.mock.calls[0][0]).toEqual(gitIgnoreFilePath);
     expect(fsMock.appendFileSync.mock.calls[0][1]).toEqual(toAppend);
   });
   test('create a new .gitignore', () => {
     fsMock.existsSync.mockImplementation(() => false);
     insertAmplifyIgnore(gitIgnoreFilePath);
-    expect(fsMock.writeFileSync.mock.calls[0][0]).toEqual('testPath');
+    expect(fsMock.writeFileSync.mock.calls[0][0]).toEqual(gitIgnoreFilePath);
     expect(fsMock.writeFileSync.mock.calls[0][1]).toEqual(toAppend.trim());
   });
+  test('legacy .gitignore files reformat themselves when accessed by a newer version of the CLI', () => {
+    fsMock.existsSync.mockImplementation(() => true);
+    fsMock.readFileSync.mockImplementation(() => 'amplify/' + os.EOL + legacyToAppend.trim());
+    insertAmplifyIgnore(gitIgnoreFilePath);
+    expect(fsMock.writeFileSync.mock.calls[0][0]).toEqual(gitIgnoreFilePath);
+    expect(fsMock.writeFileSync.mock.calls[0][1]).toEqual('amplify/');
+    expect(fsMock.appendFileSync.mock.calls[0][0]).toEqual(gitIgnoreFilePath);
+    expect(fsMock.appendFileSync.mock.calls[0][1]).toEqual(toAppend);
+  });
 });
diff --git a/packages/amplify-cli/src/extensions/amplify-helpers/git-manager.ts b/packages/amplify-cli/src/extensions/amplify-helpers/git-manager.ts
index af803131f3e..b868a37cc52 100644
--- a/packages/amplify-cli/src/extensions/amplify-helpers/git-manager.ts
+++ b/packages/amplify-cli/src/extensions/amplify-helpers/git-manager.ts
@@ -2,12 +2,16 @@ import * as fs from 'fs-extra';
 import * as os from 'os';
 import { LocalLogDirectory } from 'amplify-cli-logger';
 
-const amplifyMark = '#amplify';
+const amplifyMark = '#amplify-do-not-edit-begin';
+const amplifyEndMark = '#amplify-do-not-edit-end';
+const deprecatedAmplifyMark = '#amplify';
 const amplifyMarkRegExp = new RegExp(`^${amplifyMark}`);
+const amplifyEndMarkRegExp = new RegExp(`^${amplifyEndMark}`);
+const deprecatedAmplifyMarkRegExp = new RegExp(`^${deprecatedAmplifyMark}`);
 
 export function insertAmplifyIgnore(gitIgnoreFilePath: string): void {
   if (fs.existsSync(gitIgnoreFilePath)) {
-    removeAmplifyIgnore(gitIgnoreFilePath);
+    rebuildAmplifyIgnore(gitIgnoreFilePath);
 
     fs.appendFileSync(gitIgnoreFilePath, getGitIgnoreAppendString());
   } else {
@@ -15,7 +19,7 @@ export function insertAmplifyIgnore(gitIgnoreFilePath: string): void {
   }
 }
 
-function removeAmplifyIgnore(gitIgnoreFilePath: string): void {
+function rebuildAmplifyIgnore(gitIgnoreFilePath: string): void {
   if (fs.existsSync(gitIgnoreFilePath)) {
     let newGitIgnoreString = '';
     const gitIgnoreStringArray = fs.readFileSync(gitIgnoreFilePath, 'utf8').split(os.EOL);
@@ -26,10 +30,10 @@ function removeAmplifyIgnore(gitIgnoreFilePath: string): void {
       const newLine = gitIgnoreStringArray[i].trim();
 
       if (isInRemoval) {
-        if (newLine.length === 0) {
+        if (amplifyEndMarkRegExp.test(newLine) || newLine.length === 0) {
           isInRemoval = false;
         }
-      } else if (amplifyMarkRegExp.test(newLine)) {
+      } else if (amplifyMarkRegExp.test(newLine) || deprecatedAmplifyMarkRegExp.test(newLine)) {
         isInRemoval = true;
       } else {
         newGitIgnoreString += newLine + os.EOL;
@@ -64,7 +68,7 @@ function getGitIgnoreAppendString() {
     '.secret-*',
   ];
 
-  const toAppend = `${os.EOL + os.EOL + amplifyMark + os.EOL}${ignoreList.join(os.EOL)}`;
+  const toAppend = `${os.EOL + os.EOL + amplifyMark + os.EOL}${ignoreList.join(os.EOL)}${os.EOL + amplifyEndMark + os.EOL}`;
 
   return toAppend;
 }