diff --git a/.changeset/dirty-years-attend.md b/.changeset/dirty-years-attend.md
new file mode 100644
index 0000000000..7a1bf1a2e9
--- /dev/null
+++ b/.changeset/dirty-years-attend.md
@@ -0,0 +1,6 @@
+---
+'@aws-amplify/backend-function': patch
+'@aws-amplify/backend': patch
+---
+
+fix: Clear generated env directory before shim generation
diff --git a/packages/backend-function/src/function_env_type_generator.test.ts b/packages/backend-function/src/function_env_type_generator.test.ts
index 15a913479c..a5d85955a3 100644
--- a/packages/backend-function/src/function_env_type_generator.test.ts
+++ b/packages/backend-function/src/function_env_type_generator.test.ts
@@ -1,11 +1,15 @@
-import { describe, it, mock } from 'node:test';
+import { beforeEach, describe, it, mock } from 'node:test';
 import fs from 'fs';
 import fsp from 'fs/promises';
 import { FunctionEnvironmentTypeGenerator } from './function_env_type_generator.js';
 import assert from 'assert';
 import { pathToFileURL } from 'url';
+import path from 'path';
 
 void describe('FunctionEnvironmentTypeGenerator', () => {
+  beforeEach(() => {
+    resetFactoryGlobalState();
+  });
   void it('generates a type definition file', () => {
     const fsOpenSyncMock = mock.method(fs, 'openSync');
     const fsWriteFileSyncMock = mock.method(fs, 'writeFileSync', () => null);
@@ -101,4 +105,54 @@ void describe('FunctionEnvironmentTypeGenerator', () => {
 
     mock.restoreAll();
   });
+  void it('clears the generated env directory even if there are multiple calls', async () => {
+    const fsExistsSyncMock = mock.method(fs, 'existsSync', () => true);
+    const fsRmSyncMock = mock.method(fs, 'rmSync', () => {});
+
+    new FunctionEnvironmentTypeGenerator('testFunction1');
+
+    assert.equal(fsExistsSyncMock.mock.calls.length, 1);
+    assert.equal(fsRmSyncMock.mock.calls.length, 1);
+
+    new FunctionEnvironmentTypeGenerator('testFunction2');
+
+    assert.equal(fsExistsSyncMock.mock.calls.length, 1);
+    assert.equal(fsRmSyncMock.mock.calls.length, 1);
+
+    fsExistsSyncMock.mock.restore();
+    fsRmSyncMock.mock.restore();
+  });
+  void it("don't clear the generated env directory if it doesn't exist", async () => {
+    const fsExistsSyncMock = mock.method(fs, 'existsSync', () => false);
+    const fsRmSyncMock = mock.method(fs, 'rmSync', () => {});
+
+    new FunctionEnvironmentTypeGenerator('testFunction');
+
+    assert.equal(fsExistsSyncMock.mock.calls.length, 1);
+    assert.equal(fsRmSyncMock.mock.calls.length, 0);
+
+    fsExistsSyncMock.mock.restore();
+    fsRmSyncMock.mock.restore();
+  });
+  void it('ensure correct directory is deleted', async () => {
+    const pathToDelete = path.join(
+      process.cwd(),
+      '.amplify',
+      'generated',
+      'env'
+    );
+    const fsExistsSyncMock = mock.method(fs, 'existsSync', () => true);
+    const fsRmSyncMock = mock.method(fs, 'rmSync', () => {});
+
+    new FunctionEnvironmentTypeGenerator('testFunction');
+
+    assert.equal(fsExistsSyncMock.mock.calls.length, 1);
+    assert.equal(fsRmSyncMock.mock.calls[0].arguments[0], pathToDelete);
+
+    fsExistsSyncMock.mock.restore();
+    fsRmSyncMock.mock.restore();
+  });
+  const resetFactoryGlobalState = () => {
+    FunctionEnvironmentTypeGenerator.isEnvDirectoryInitialized = false;
+  };
 });
diff --git a/packages/backend-function/src/function_env_type_generator.ts b/packages/backend-function/src/function_env_type_generator.ts
index d01a701a19..162c5ecd37 100644
--- a/packages/backend-function/src/function_env_type_generator.ts
+++ b/packages/backend-function/src/function_env_type_generator.ts
@@ -7,10 +7,11 @@ import { EOL } from 'os';
  * Generates a typed process.env shim for environment variables
  */
 export class FunctionEnvironmentTypeGenerator {
+  // Using this to ensure directory is cleared once per synthesis
+  static isEnvDirectoryInitialized = false;
   private readonly header =
     '// This file is auto-generated by Amplify. Edits will be overwritten.';
 
-  // The variable gets updated when the fully typed file is updated.
   private readonly envAssignment = 'export const env = process.env';
 
   private typeDefFilePath: string;
@@ -21,9 +22,14 @@ export class FunctionEnvironmentTypeGenerator {
    * Initialize typed process.env shim file name and location
    */
   constructor(private readonly functionName: string) {
-    this.typeDefFilePath = `${process.cwd()}/.amplify/generated/env/${
-      this.functionName
-    }.ts`;
+    this.typeDefFilePath = path.join(
+      process.cwd(),
+      '.amplify',
+      'generated',
+      'env',
+      `${this.functionName}.ts`
+    );
+    this.clearGeneratedEnvDirectory();
   }
 
   /**
@@ -97,4 +103,22 @@ export class FunctionEnvironmentTypeGenerator {
 
     fs.writeFileSync(this.typeDefFilePath, content);
   };
+  /**
+   * Clear existing files and subdirectories in the generated env directory
+   */
+  private clearGeneratedEnvDirectory = (): void => {
+    if (FunctionEnvironmentTypeGenerator.isEnvDirectoryInitialized) {
+      return;
+    }
+    const pathToDelete = path.join(
+      process.cwd(),
+      '.amplify',
+      'generated',
+      'env'
+    );
+    if (fs.existsSync(pathToDelete)) {
+      fs.rmSync(pathToDelete, { recursive: true, force: true });
+      FunctionEnvironmentTypeGenerator.isEnvDirectoryInitialized = true;
+    }
+  };
 }