diff --git a/packages/aws-cdk/lib/commands/flags/operations.ts b/packages/aws-cdk/lib/commands/flags/operations.ts
index 28a574cbe..b08d26476 100644
--- a/packages/aws-cdk/lib/commands/flags/operations.ts
+++ b/packages/aws-cdk/lib/commands/flags/operations.ts
@@ -43,6 +43,8 @@ export class FlagOperations {
   private allStacks: CloudFormationStackArtifact[];
   private queue: PQueue;
   private baselineTempDir?: string;
+  private originalTempDir?: string;
+  private modifiedTempDir?: string;
 
   constructor(
     private readonly flags: FeatureFlag[],
@@ -278,21 +280,26 @@ export class FlagOperations {
     const cdkJson = await JSON.parse(await fs.readFile(path.join(process.cwd(), 'cdk.json'), 'utf-8'));
     const app = cdkJson.app;
 
+    this.originalTempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cdk-original-'));
     const source = await this.toolkit.fromCdkApp(app, {
       contextStore: memoryContext,
-      outdir: fs.mkdtempSync(path.join(os.tmpdir(), 'cdk-original-')),
+      outdir: this.originalTempDir,
     });
 
     const updateObj = await this.buildUpdateObject(flagNames, params, baseContextValues);
-    if (!updateObj) return false;
+    if (!updateObj) {
+      await this.cleanupTempDirectories();
+      return false;
+    }
 
     await memoryContext.update(updateObj);
     const cx = await this.toolkit.synth(source);
     const assembly = cx.cloudAssembly;
 
+    this.modifiedTempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cdk-temp-'));
     const modifiedSource = await this.toolkit.fromCdkApp(app, {
       contextStore: memoryContext,
-      outdir: fs.mkdtempSync(path.join(os.tmpdir(), 'cdk-temp-')),
+      outdir: this.modifiedTempDir,
     });
 
     const modifiedCx = await this.toolkit.synth(modifiedSource);
@@ -378,10 +385,14 @@ export class FlagOperations {
 
   /** Removes temporary directories created during flag operations */
   private async cleanupTempDirectories(): Promise<void> {
-    const originalDir = path.join(process.cwd(), 'original');
-    const tempDir = path.join(process.cwd(), 'temp');
-    await fs.remove(originalDir);
-    await fs.remove(tempDir);
+    if (this.originalTempDir) {
+      await fs.remove(this.originalTempDir);
+      this.originalTempDir = undefined;
+    }
+    if (this.modifiedTempDir) {
+      await fs.remove(this.modifiedTempDir);
+      this.modifiedTempDir = undefined;
+    }
   }
 
   /** Actually modifies the cdk.json file with the new flag values */
diff --git a/packages/aws-cdk/test/commands/flag-operations.test.ts b/packages/aws-cdk/test/commands/flag-operations.test.ts
index a52bb0b11..1297b768b 100644
--- a/packages/aws-cdk/test/commands/flag-operations.test.ts
+++ b/packages/aws-cdk/test/commands/flag-operations.test.ts
@@ -430,6 +430,66 @@ describe('processFlagsCommand', () => {
     requestResponseSpy.mockRestore();
   });
 
+  test('cleans up the real temp directories created during prototyping when the user cancels', async () => {
+    // Regression test: cleanupTempDirectories() used to delete
+    // `${cwd}/original` and `${cwd}/temp`, but the directories actually
+    // created by prototypeChanges() are `mkdtemp`-generated paths under
+    // os.tmpdir() (prefixed `cdk-original-`/`cdk-temp-`). Those paths were
+    // never stored anywhere, so every `cdk flags --set` invocation leaked
+    // two real synthesized-cloud-assembly directories into the OS temp dir.
+    const cdkJsonPath = await createCdkJsonFile();
+    setupMockToolkitForPrototyping(mockToolkit);
+
+    const tmpEntriesBefore = fs.readdirSync(os.tmpdir());
+
+    const requestResponseSpy = jest.spyOn(ioHelper, 'requestResponse');
+    requestResponseSpy.mockResolvedValue(false);
+
+    const options: FlagsOptions = {
+      FLAGNAME: ['@aws-cdk/core:testFlag'],
+      set: true,
+      value: 'true',
+    };
+
+    const flagOperations = new FlagCommandHandler(mockFlagsData, ioHelper, options, mockToolkit);
+    await expect(flagOperations.processFlagsCommand()).rejects.toThrow('Flag update cancelled');
+
+    const leakedEntries = fs.readdirSync(os.tmpdir())
+      .filter(entry => !tmpEntriesBefore.includes(entry))
+      .filter(entry => entry.startsWith('cdk-original-') || entry.startsWith('cdk-temp-'));
+    expect(leakedEntries).toEqual([]);
+
+    await cleanupCdkJsonFile(cdkJsonPath);
+    requestResponseSpy.mockRestore();
+  });
+
+  test('cleans up the real temp directories created during prototyping when the user accepts', async () => {
+    const cdkJsonPath = await createCdkJsonFile();
+    setupMockToolkitForPrototyping(mockToolkit);
+
+    const tmpEntriesBefore = fs.readdirSync(os.tmpdir());
+
+    const requestResponseSpy = jest.spyOn(ioHelper, 'requestResponse');
+    requestResponseSpy.mockResolvedValue(true);
+
+    const options: FlagsOptions = {
+      FLAGNAME: ['@aws-cdk/core:testFlag'],
+      set: true,
+      value: 'true',
+    };
+
+    const flagOperations = new FlagCommandHandler(mockFlagsData, ioHelper, options, mockToolkit);
+    await flagOperations.processFlagsCommand();
+
+    const leakedEntries = fs.readdirSync(os.tmpdir())
+      .filter(entry => !tmpEntriesBefore.includes(entry))
+      .filter(entry => entry.startsWith('cdk-original-') || entry.startsWith('cdk-temp-'));
+    expect(leakedEntries).toEqual([]);
+
+    await cleanupCdkJsonFile(cdkJsonPath);
+    requestResponseSpy.mockRestore();
+  });
+
   test('does not resynthesize when setting flag to same value as current context', async () => {
     const cdkJsonPath = await createCdkJsonFile({
       '@aws-cdk/core:testFlag': true,