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/package-lock.json b/package-lock.json
index ba819efd32..a2913bd8dc 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23297,6 +23297,7 @@
       "version": "11.2.0",
       "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-11.2.0.tgz",
       "integrity": "sha512-PmDi3uwK5nFuXh7XDTlVnS17xJS7vW36is2+w3xcv8SVxiB4NyATf4ctkVY5bkSjX0Y4nbvZCq1/EjtEyr9ktw==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "graceful-fs": "^4.2.0",
@@ -23971,6 +23972,7 @@
       "version": "9.0.6",
       "resolved": "https://registry.npmjs.org/immer/-/immer-9.0.6.tgz",
       "integrity": "sha512-G95ivKpy+EvVAnAab4fVa4YGYn24J1SpEktnJX7JJ45Bd7xqME/SCplFzYFmTbrkwZbQ4xJK1xMTUYBkN6pWsQ==",
+      "dev": true,
       "license": "MIT",
       "funding": {
         "type": "opencollective",
@@ -30147,6 +30149,7 @@
       "version": "8.3.2",
       "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
       "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
+      "dev": true,
       "license": "MIT",
       "bin": {
         "uuid": "dist/bin/uuid"
@@ -30930,17 +30933,17 @@
       }
     },
     "packages/ampx": {
-      "version": "0.2.1",
+      "version": "0.2.2",
       "license": "Apache-2.0"
     },
     "packages/auth-construct": {
       "name": "@aws-amplify/auth-construct",
-      "version": "1.3.0",
+      "version": "1.3.1",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.1.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/backend-output-storage": "^1.1.2",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "@aws-sdk/util-arn-parser": "^3.568.0"
       },
       "peerDependencies": {
@@ -30950,20 +30953,20 @@
     },
     "packages/backend": {
       "name": "@aws-amplify/backend",
-      "version": "1.2.1",
+      "version": "1.3.0",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/backend-auth": "^1.1.2",
-        "@aws-amplify/backend-data": "^1.1.3",
-        "@aws-amplify/backend-function": "^1.4.0",
+        "@aws-amplify/backend-auth": "^1.2.0",
+        "@aws-amplify/backend-data": "^1.1.4",
+        "@aws-amplify/backend-function": "^1.5.0",
         "@aws-amplify/backend-output-schemas": "^1.2.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
-        "@aws-amplify/backend-secret": "^1.0.1",
-        "@aws-amplify/backend-storage": "^1.1.1",
-        "@aws-amplify/client-config": "^1.3.0",
+        "@aws-amplify/backend-output-storage": "^1.1.2",
+        "@aws-amplify/backend-secret": "^1.1.2",
+        "@aws-amplify/backend-storage": "^1.2.0",
+        "@aws-amplify/client-config": "^1.3.1",
         "@aws-amplify/data-schema": "^1.0.0",
         "@aws-amplify/platform-core": "^1.1.0",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.3.0",
         "@aws-sdk/client-amplify": "^3.624.0",
         "lodash.snakecase": "^4.1.1"
       },
@@ -30996,15 +30999,15 @@
     },
     "packages/backend-auth": {
       "name": "@aws-amplify/backend-auth",
-      "version": "1.1.4",
+      "version": "1.2.0",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/auth-construct": "^1.3.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
-        "@aws-amplify/plugin-types": "^1.2.1"
+        "@aws-amplify/auth-construct": "^1.3.1",
+        "@aws-amplify/backend-output-storage": "^1.1.2",
+        "@aws-amplify/plugin-types": "^1.3.0"
       },
       "devDependencies": {
-        "@aws-amplify/backend-platform-test-stubs": "^0.3.4",
+        "@aws-amplify/backend-platform-test-stubs": "^0.3.5",
         "@aws-amplify/platform-core": "^1.0.6"
       },
       "peerDependencies": {
@@ -31014,17 +31017,17 @@
     },
     "packages/backend-data": {
       "name": "@aws-amplify/backend-data",
-      "version": "1.1.3",
+      "version": "1.1.4",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.1.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
+        "@aws-amplify/backend-output-storage": "^1.1.2",
         "@aws-amplify/data-construct": "^1.10.1",
         "@aws-amplify/data-schema-types": "^1.1.1",
-        "@aws-amplify/plugin-types": "^1.2.1"
+        "@aws-amplify/plugin-types": "^1.2.2"
       },
       "devDependencies": {
-        "@aws-amplify/backend-platform-test-stubs": "^0.3.4",
+        "@aws-amplify/backend-platform-test-stubs": "^0.3.5",
         "@aws-amplify/data-schema": "^1.0.0",
         "@aws-amplify/platform-core": "^1.0.7"
       },
@@ -31035,11 +31038,11 @@
     },
     "packages/backend-deployer": {
       "name": "@aws-amplify/backend-deployer",
-      "version": "1.1.2",
+      "version": "1.1.4",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/platform-core": "^1.0.6",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "execa": "^8.0.1",
         "tsx": "^4.6.1"
       },
@@ -31050,16 +31053,16 @@
     },
     "packages/backend-function": {
       "name": "@aws-amplify/backend-function",
-      "version": "1.4.0",
+      "version": "1.5.0",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.1.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/backend-output-storage": "^1.1.2",
+        "@aws-amplify/plugin-types": "^1.3.0",
         "execa": "^8.0.1"
       },
       "devDependencies": {
-        "@aws-amplify/backend-platform-test-stubs": "^0.3.4",
+        "@aws-amplify/backend-platform-test-stubs": "^0.3.5",
         "@aws-amplify/platform-core": "^1.1.0",
         "@aws-sdk/client-ssm": "^3.624.0",
         "aws-sdk": "^2.1550.0",
@@ -31097,12 +31100,12 @@
     },
     "packages/backend-output-storage": {
       "name": "@aws-amplify/backend-output-storage",
-      "version": "1.1.1",
+      "version": "1.1.2",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.2.0",
         "@aws-amplify/platform-core": "^1.0.6",
-        "@aws-amplify/plugin-types": "^1.2.1"
+        "@aws-amplify/plugin-types": "^1.2.2"
       },
       "peerDependencies": {
         "aws-cdk-lib": "^2.152.0"
@@ -31110,21 +31113,21 @@
     },
     "packages/backend-platform-test-stubs": {
       "name": "@aws-amplify/backend-platform-test-stubs",
-      "version": "0.3.4",
+      "version": "0.3.5",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "aws-cdk-lib": "^2.152.0",
         "constructs": "^10.0.0"
       }
     },
     "packages/backend-secret": {
       "name": "@aws-amplify/backend-secret",
-      "version": "1.1.1",
+      "version": "1.1.3",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/platform-core": "^1.0.5",
-        "@aws-amplify/plugin-types": "^1.1.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "@aws-sdk/client-ssm": "^3.624.0"
       },
       "devDependencies": {
@@ -31133,15 +31136,15 @@
     },
     "packages/backend-storage": {
       "name": "@aws-amplify/backend-storage",
-      "version": "1.1.2",
+      "version": "1.2.0",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.2.0",
-        "@aws-amplify/backend-output-storage": "^1.1.1",
-        "@aws-amplify/plugin-types": "^1.2.1"
+        "@aws-amplify/backend-output-storage": "^1.1.2",
+        "@aws-amplify/plugin-types": "^1.3.0"
       },
       "devDependencies": {
-        "@aws-amplify/backend-platform-test-stubs": "^0.3.4",
+        "@aws-amplify/backend-platform-test-stubs": "^0.3.5",
         "@aws-amplify/platform-core": "^1.0.6"
       },
       "peerDependencies": {
@@ -31151,21 +31154,21 @@
     },
     "packages/cli": {
       "name": "@aws-amplify/backend-cli",
-      "version": "1.2.6",
+      "version": "1.2.8",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/backend-deployer": "^1.1.1",
+        "@aws-amplify/backend-deployer": "^1.1.3",
         "@aws-amplify/backend-output-schemas": "^1.1.0",
-        "@aws-amplify/backend-secret": "^1.1.0",
-        "@aws-amplify/cli-core": "^1.1.2",
-        "@aws-amplify/client-config": "^1.2.1",
-        "@aws-amplify/deployed-backend-client": "^1.3.0",
-        "@aws-amplify/form-generator": "^1.0.1",
-        "@aws-amplify/model-generator": "^1.0.5",
+        "@aws-amplify/backend-secret": "^1.1.2",
+        "@aws-amplify/cli-core": "^1.1.3",
+        "@aws-amplify/client-config": "^1.3.1",
+        "@aws-amplify/deployed-backend-client": "^1.4.1",
+        "@aws-amplify/form-generator": "^1.0.3",
+        "@aws-amplify/model-generator": "^1.0.8",
         "@aws-amplify/platform-core": "^1.0.5",
-        "@aws-amplify/plugin-types": "^1.2.1",
-        "@aws-amplify/sandbox": "^1.2.0",
-        "@aws-amplify/schema-generator": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.3.0",
+        "@aws-amplify/sandbox": "^1.2.2",
+        "@aws-amplify/schema-generator": "^1.2.4",
         "@aws-sdk/client-amplify": "^3.624.0",
         "@aws-sdk/client-cloudformation": "^3.624.0",
         "@aws-sdk/client-s3": "^3.624.0",
@@ -31198,7 +31201,7 @@
     },
     "packages/cli-core": {
       "name": "@aws-amplify/cli-core",
-      "version": "1.1.2",
+      "version": "1.1.3",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/platform-core": "^1.0.5",
@@ -31305,14 +31308,14 @@
     },
     "packages/client-config": {
       "name": "@aws-amplify/client-config",
-      "version": "1.3.0",
+      "version": "1.3.2",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.2.0",
-        "@aws-amplify/deployed-backend-client": "^1.4.0",
-        "@aws-amplify/model-generator": "^1.0.5",
+        "@aws-amplify/deployed-backend-client": "^1.4.1",
+        "@aws-amplify/model-generator": "^1.0.7",
         "@aws-amplify/platform-core": "^1.0.7",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "zod": "^3.22.2"
       },
       "devDependencies": {
@@ -31327,12 +31330,12 @@
       }
     },
     "packages/create-amplify": {
-      "version": "1.0.5",
+      "version": "1.0.6",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/cli-core": "^1.1.1",
+        "@aws-amplify/cli-core": "^1.1.3",
         "@aws-amplify/platform-core": "^1.0.3",
-        "@aws-amplify/plugin-types": "^1.1.0",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "execa": "^8.0.1",
         "kleur": "^4.1.5",
         "yargs": "^17.7.2"
@@ -31442,12 +31445,12 @@
     },
     "packages/deployed-backend-client": {
       "name": "@aws-amplify/deployed-backend-client",
-      "version": "1.4.0",
+      "version": "1.4.1",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.2.0",
         "@aws-amplify/platform-core": "^1.0.5",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "zod": "^3.22.2"
       },
       "peerDependencies": {
@@ -31470,7 +31473,7 @@
     },
     "packages/form-generator": {
       "name": "@aws-amplify/form-generator",
-      "version": "1.0.1",
+      "version": "1.0.3",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/appsync-modelgen-plugin": "^2.11.0",
@@ -31490,20 +31493,20 @@
     },
     "packages/integration-tests": {
       "name": "@aws-amplify/integration-tests",
-      "version": "0.5.8",
+      "version": "0.5.9",
       "license": "Apache-2.0",
       "devDependencies": {
         "@apollo/client": "^3.10.1",
         "@aws-amplify/ai-constructs": "^0.1.0",
-        "@aws-amplify/auth-construct": "^1.2.2",
-        "@aws-amplify/backend": "^1.2.1",
+        "@aws-amplify/auth-construct": "^1.3.1",
+        "@aws-amplify/backend": "^1.2.2",
         "@aws-amplify/backend-ai": "^0.1.0",
-        "@aws-amplify/backend-secret": "^1.0.1",
-        "@aws-amplify/client-config": "^1.1.3",
+        "@aws-amplify/backend-secret": "^1.1.2",
+        "@aws-amplify/client-config": "^1.3.1",
         "@aws-amplify/data-schema": "^1.0.0",
-        "@aws-amplify/deployed-backend-client": "^1.3.0",
+        "@aws-amplify/deployed-backend-client": "^1.4.1",
         "@aws-amplify/platform-core": "^1.1.0",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "@aws-sdk/client-accessanalyzer": "^3.624.0",
         "@aws-sdk/client-amplify": "^3.624.0",
         "@aws-sdk/client-bedrock-runtime": "^3.622.0",
@@ -31549,15 +31552,15 @@
     },
     "packages/model-generator": {
       "name": "@aws-amplify/model-generator",
-      "version": "1.0.6",
+      "version": "1.0.8",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/backend-output-schemas": "^1.1.0",
-        "@aws-amplify/deployed-backend-client": "^1.3.0",
+        "@aws-amplify/deployed-backend-client": "^1.4.1",
         "@aws-amplify/graphql-generator": "^0.4.0",
         "@aws-amplify/graphql-types-generator": "^3.6.0",
         "@aws-amplify/platform-core": "^1.0.5",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.3.0",
         "@aws-sdk/client-appsync": "^3.624.0",
         "@aws-sdk/client-s3": "^3.624.0",
         "@aws-sdk/credential-providers": "^3.624.0",
@@ -31603,7 +31606,7 @@
     },
     "packages/plugin-types": {
       "name": "@aws-amplify/plugin-types",
-      "version": "1.2.1",
+      "version": "1.3.0",
       "license": "Apache-2.0",
       "devDependencies": {
         "execa": "^5.1.1"
@@ -31732,16 +31735,16 @@
     },
     "packages/sandbox": {
       "name": "@aws-amplify/sandbox",
-      "version": "1.2.1",
+      "version": "1.2.2",
       "license": "Apache-2.0",
       "dependencies": {
-        "@aws-amplify/backend-deployer": "^1.1.0",
-        "@aws-amplify/backend-secret": "^1.1.1",
-        "@aws-amplify/cli-core": "^1.1.2",
-        "@aws-amplify/client-config": "^1.1.3",
-        "@aws-amplify/deployed-backend-client": "^1.3.0",
+        "@aws-amplify/backend-deployer": "^1.1.3",
+        "@aws-amplify/backend-secret": "^1.1.2",
+        "@aws-amplify/cli-core": "^1.1.3",
+        "@aws-amplify/client-config": "^1.3.1",
+        "@aws-amplify/deployed-backend-client": "^1.4.1",
         "@aws-amplify/platform-core": "^1.0.6",
-        "@aws-amplify/plugin-types": "^1.2.1",
+        "@aws-amplify/plugin-types": "^1.2.2",
         "@aws-sdk/client-cloudformation": "^3.624.0",
         "@aws-sdk/client-cloudwatch-logs": "^3.624.0",
         "@aws-sdk/client-lambda": "^3.624.0",
@@ -31765,7 +31768,7 @@
     },
     "packages/schema-generator": {
       "name": "@aws-amplify/schema-generator",
-      "version": "1.2.2",
+      "version": "1.2.4",
       "license": "Apache-2.0",
       "dependencies": {
         "@aws-amplify/graphql-schema-generator": "^0.9.4",
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 d988e06fec..97fad7f0fe 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);
@@ -69,4 +73,54 @@ void describe('FunctionEnvironmentTypeGenerator', () => {
 
     await fsp.rm(targetDirectory, { recursive: true, force: true });
   });
+  void it('clears the generated env directory', 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 ea650e26c9..7302bc75ba 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();
   }
 
   /**
@@ -93,4 +99,22 @@ 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;
+    }
+  };
 }