diff --git a/packages/e2e/tests/app-basic-flow.spec.ts b/packages/e2e/tests/app-basic-flow.spec.ts
new file mode 100644
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+++ b/packages/e2e/tests/app-basic-flow.spec.ts
@@ -0,0 +1,158 @@
+/* eslint-disable no-restricted-imports */
+import {
+  appTestFixture as test,
+  createApp,
+  extractClientId,
+  deployApp,
+  versionsList,
+  configLink,
+  teardownApp,
+} from '../setup/app.js'
+import {requireEnv} from '../setup/env.js'
+import {expect} from '@playwright/test'
+import * as fs from 'fs'
+import * as path from 'path'
+
+/**
+ * App basic flow — from scratch (QA checklist: Apps section, no extensions).
+ *
+ * Exercises the full app lifecycle end-to-end:
+ *   1. Create a new app from the reactRouter template
+ *   2. Start dev server
+ *   3. Run a GraphQL query via app execute
+ *   4. Quit dev server with q
+ *   5. Clean dev preview
+ *   6. Deploy with a version tag
+ *   7. Verify version in versions list
+ *   8. Create a secondary app, config link to it
+ *   9. Deploy to the secondary app
+ */
+test.describe('App basic flow — from scratch', () => {
+  test('init, dev, execute, quit, clean, deploy, versions, config link, deploy to secondary', async ({
+    cli,
+    env,
+    browserPage,
+  }) => {
+    test.setTimeout(15 * 60 * 1000)
+    requireEnv(env, 'orgId', 'storeFqdn')
+
+    const parentDir = fs.mkdtempSync(path.join(env.tempDir, 'app-'))
+    const appName = `E2E-basic-${Date.now()}`
+    let secondaryParentDir = ''
+    const secondaryAppName = `E2E-basic2-${Date.now()}`
+
+    try {
+      // Step 1: Create a new app
+      const initResult = await createApp({
+        cli,
+        parentDir,
+        name: appName,
+        template: 'reactRouter',
+        flavor: 'typescript',
+        packageManager: 'npm',
+        orgId: env.orgId,
+      })
+      expect(initResult.exitCode, `Step 1 - app init failed:\n${initResult.stderr}`).toBe(0)
+      const appDir = initResult.appDir
+
+      // Step 2: Start dev server (CI='' enables keyboard shortcuts)
+      const dev = await cli.spawn(['app', 'dev', '--path', appDir], {env: {CI: ''}})
+      try {
+        await dev.waitForOutput('Ready, watching for changes in your app', 3 * 60 * 1000)
+
+        // Step 3: Run a GraphQL query
+        const executeResult = await cli.exec(
+          ['app', 'execute', '--query', 'query { shop { name } }', '--path', appDir],
+          {timeout: 60 * 1000},
+        )
+        const executeOutput = executeResult.stdout + executeResult.stderr
+        expect(executeResult.exitCode, `Step 3 - app execute failed:\n${executeOutput}`).toBe(0)
+        expect(executeOutput, 'Step 3 - app execute: response missing "shop" field').toContain('shop')
+
+        // Step 4: Quit dev server
+        dev.sendKey('q')
+        const devExitCode = await dev.waitForExit(30_000)
+        expect(devExitCode, 'Step 4 - app dev quit failed').toBe(0)
+      } finally {
+        dev.kill()
+      }
+
+      // Step 5: Clean dev preview
+      const cleanResult = await cli.exec(['app', 'dev', 'clean', '--path', appDir])
+      const cleanOutput = cleanResult.stdout + cleanResult.stderr
+      expect(cleanResult.exitCode, `Step 5 - app dev clean failed:\n${cleanOutput}`).toBe(0)
+      expect(cleanOutput, 'Step 5 - missing "Dev preview stopped"').toContain('Dev preview stopped')
+
+      // Step 6: Deploy with a version tag
+      const versionTag = `E2E-v1-${Date.now()}`
+      const deployResult = await deployApp({
+        cli,
+        appDir,
+        version: versionTag,
+        message: 'E2E basic flow deployment',
+      })
+      expect(deployResult.exitCode, `Step 6 - app deploy failed:\n${deployResult.stderr}`).toBe(0)
+
+      // Step 7: Verify version in list
+      const listResult = await versionsList({cli, appDir})
+      const listOutput = listResult.stdout + listResult.stderr
+      expect(listResult.exitCode, `Step 7 - versions list failed:\n${listOutput}`).toBe(0)
+      expect(listOutput, `Step 7 - version tag "${versionTag}" not found`).toContain(versionTag)
+
+      // Step 8: Create a secondary app and config link to it
+      secondaryParentDir = fs.mkdtempSync(path.join(env.tempDir, 'app-'))
+      const secondaryInit = await createApp({
+        cli,
+        parentDir: secondaryParentDir,
+        name: secondaryAppName,
+        template: 'reactRouter',
+        flavor: 'typescript',
+        packageManager: 'npm',
+        orgId: env.orgId,
+      })
+      expect(secondaryInit.exitCode, `Step 8a - secondary app init failed:\n${secondaryInit.stderr}`).toBe(0)
+
+      const secondaryClientId = extractClientId(secondaryInit.appDir)
+
+      // Write a TOML stub so config link skips the "Configuration file name" prompt
+      fs.writeFileSync(path.join(appDir, 'shopify.app.secondary.toml'), `client_id = "${secondaryClientId}"\n`)
+
+      const linkResult = await configLink({cli, appDir, clientId: secondaryClientId})
+      const linkOutput = linkResult.stdout + linkResult.stderr
+      expect(linkResult.exitCode, `Step 8b - config link failed:\n${linkOutput}`).toBe(0)
+      expect(linkOutput, 'Step 8b - missing "is now linked to"').toContain('is now linked to')
+
+      // Step 9: Deploy to the secondary app
+      const tomlFiles = fs
+        .readdirSync(appDir)
+        .filter(
+          (file: string) => file.startsWith('shopify.app.') && file.endsWith('.toml') && file !== 'shopify.app.toml',
+        )
+      const secondaryConfig = tomlFiles[0]?.replace('shopify.app.', '').replace('.toml', '') ?? 'secondary'
+      const secondaryVersionTag = `E2E-v2-${Date.now()}`
+      const secondaryDeployResult = await deployApp({
+        cli,
+        appDir,
+        config: secondaryConfig,
+        version: secondaryVersionTag,
+        message: 'E2E secondary deployment',
+      })
+      expect(secondaryDeployResult.exitCode, `Step 9 - secondary deploy failed:\n${secondaryDeployResult.stderr}`).toBe(
+        0,
+      )
+    } finally {
+      // E2E_SKIP_CLEANUP=1 skips cleanup for debugging. Run `pnpm test:e2e-cleanup` afterward.
+      if (!process.env.E2E_SKIP_CLEANUP) {
+        fs.rmSync(parentDir, {recursive: true, force: true})
+        if (secondaryParentDir) fs.rmSync(secondaryParentDir, {recursive: true, force: true})
+        await teardownApp({browserPage, appName, email: process.env.E2E_ACCOUNT_EMAIL, orgId: env.orgId})
+        await teardownApp({
+          browserPage,
+          appName: secondaryAppName,
+          email: process.env.E2E_ACCOUNT_EMAIL,
+          orgId: env.orgId,
+        })
+      }
+    }
+  })
+})