diff --git a/code/lib/cli-storybook/src/ai/index.ts b/code/lib/cli-storybook/src/ai/index.ts
index f1371c2ce921..abaf21b30b9f 100644
--- a/code/lib/cli-storybook/src/ai/index.ts
+++ b/code/lib/cli-storybook/src/ai/index.ts
@@ -46,6 +46,8 @@ export async function aiSetup(options: AiSetupOptions): Promise<void> {
     const detectedLanguage = await projectTypeService.detectLanguage();
     const language = detectedLanguage === SupportedLanguage.TYPESCRIPT ? 'ts' : 'js';
 
+    const needsUserOnboarding = await cache.get('onboarding-pending');
+
     projectInfo = {
       storybookVersion: data.versionInstalled,
       majorVersion,
@@ -60,6 +62,7 @@ export async function aiSetup(options: AiSetupOptions): Promise<void> {
       packageManagerName: getPrettyPackageManagerName(data.packageManager.type),
       language,
       hasCsfFactoryPreview: data.hasCsfFactoryPreview,
+      needsUserOnboarding,
     };
   } catch (err) {
     logger.error(
diff --git a/code/lib/cli-storybook/src/ai/setup-prompts/monorepo.ts b/code/lib/cli-storybook/src/ai/setup-prompts/monorepo.ts
index b73e3f3e8656..3b8ae0f7147e 100644
--- a/code/lib/cli-storybook/src/ai/setup-prompts/monorepo.ts
+++ b/code/lib/cli-storybook/src/ai/setup-prompts/monorepo.ts
@@ -28,7 +28,8 @@ import {
 } from './partials/rules.ts';
 
 export function instructions(projectInfo: ProjectInfo): string {
-  const { configDir, language, packageManager, packageManagerName } = projectInfo;
+  const { configDir, language, needsUserOnboarding, packageManager, packageManagerName } =
+    projectInfo;
   const tsx = ext(language, true);
   const ts = ext(language, false);
   const docsUrl = (path: string) => getDocsMarkdownUrl(path, projectInfo);
@@ -41,6 +42,7 @@ export function instructions(projectInfo: ProjectInfo): string {
     configDir,
     docsUrl,
     mswInstall,
+    needsUserOnboarding,
     packageManager,
     packageManagerName,
     tsx,
diff --git a/code/lib/cli-storybook/src/ai/setup-prompts/optimized-tests.ts b/code/lib/cli-storybook/src/ai/setup-prompts/optimized-tests.ts
index ac80395fd469..4f7dc1e1577d 100644
--- a/code/lib/cli-storybook/src/ai/setup-prompts/optimized-tests.ts
+++ b/code/lib/cli-storybook/src/ai/setup-prompts/optimized-tests.ts
@@ -26,7 +26,8 @@ import {
 } from './partials/rules.ts';
 
 export function instructions(projectInfo: ProjectInfo): string {
-  const { configDir, language, packageManager, packageManagerName } = projectInfo;
+  const { configDir, language, needsUserOnboarding, packageManager, packageManagerName } =
+    projectInfo;
   const tsx = ext(language, true);
   const ts = ext(language, false);
   const docsUrl = (path: string) => getDocsMarkdownUrl(path, projectInfo);
@@ -39,6 +40,7 @@ export function instructions(projectInfo: ProjectInfo): string {
     configDir,
     docsUrl,
     mswInstall,
+    needsUserOnboarding,
     packageManager,
     packageManagerName,
     tsx,
diff --git a/code/lib/cli-storybook/src/ai/setup-prompts/partials/steps.ts b/code/lib/cli-storybook/src/ai/setup-prompts/partials/steps.ts
index 8b18a432a65b..0233a83ff338 100644
--- a/code/lib/cli-storybook/src/ai/setup-prompts/partials/steps.ts
+++ b/code/lib/cli-storybook/src/ai/setup-prompts/partials/steps.ts
@@ -83,12 +83,16 @@ export function verifyStep(
 }
 
 export function cleanupStep(
-  projectInfo: ProjectInfo,
+  { needsUserOnboarding }: ProjectInfo,
   ctx: InstructionsContext
 ): { title: string; body: string } {
+  const onboardingInstructions = needsUserOnboarding
+    ? 'You must preserve the components, CSS, stories and MDX docs initially created by Storybook, as they are required for user onboarding in the UI.'
+    : 'Delete the components, CSS, stories and MDX docs initially created by Storybook only if you managed to write successful stories.';
+
   return {
     title: `Clean up`,
-    body: `Before finishing, remove debug code, broad mocks added during diagnosis, unused deps, and eval artifacts.`,
+    body: `Before finishing, remove debug code, broad mocks added during diagnosis, unused deps, and eval artifacts. ${onboardingInstructions}`,
   };
 }
 
diff --git a/code/lib/cli-storybook/src/ai/setup-prompts/relaxed-limits.ts b/code/lib/cli-storybook/src/ai/setup-prompts/relaxed-limits.ts
index eb7bca072429..5fdb96fff09d 100644
--- a/code/lib/cli-storybook/src/ai/setup-prompts/relaxed-limits.ts
+++ b/code/lib/cli-storybook/src/ai/setup-prompts/relaxed-limits.ts
@@ -26,7 +26,8 @@ import {
 } from './partials/rules.ts';
 
 export function instructions(projectInfo: ProjectInfo): string {
-  const { configDir, language, packageManager, packageManagerName } = projectInfo;
+  const { configDir, language, needsUserOnboarding, packageManager, packageManagerName } =
+    projectInfo;
   const tsx = ext(language, true);
   const ts = ext(language, false);
   const docsUrl = (path: string) => getDocsMarkdownUrl(path, projectInfo);
@@ -39,6 +40,7 @@ export function instructions(projectInfo: ProjectInfo): string {
     configDir,
     docsUrl,
     mswInstall,
+    needsUserOnboarding,
     packageManager,
     packageManagerName,
     tsx,
diff --git a/code/lib/cli-storybook/src/ai/types.ts b/code/lib/cli-storybook/src/ai/types.ts
index c9663ae0d6ac..239b8acbef95 100644
--- a/code/lib/cli-storybook/src/ai/types.ts
+++ b/code/lib/cli-storybook/src/ai/types.ts
@@ -29,12 +29,15 @@ export interface ProjectInfo {
   packageManagerName?: string;
   /** Whether the project's preview file uses the CSF Factory format. */
   hasCsfFactoryPreview: boolean;
+  /** Whether the user has requested to be onboarded into Storybook. */
+  needsUserOnboarding: boolean;
 }
 
 export interface SetupInstructionsContext {
   configDir: string;
   docsUrl: (path: string) => string;
   mswInstall: string;
+  needsUserOnboarding: boolean;
   packageManager: JsPackageManager;
   packageManagerName: string | undefined;
   tsx: string;