diff --git a/.github/workflows/tests-pr.yml b/.github/workflows/tests-pr.yml
index 657d8f2a91f..952d0b24ef4 100644
--- a/.github/workflows/tests-pr.yml
+++ b/.github/workflows/tests-pr.yml
@@ -317,6 +317,7 @@ jobs:
           E2E_ACCOUNT_PASSWORD: ${{ secrets.E2E_ACCOUNT_PASSWORD }}
           E2E_STORE_FQDN: ${{ secrets.E2E_STORE_FQDN }}
           E2E_SECONDARY_CLIENT_ID: ${{ secrets.E2E_SECONDARY_CLIENT_ID }}
+          E2E_ORG_ID: ${{ secrets.E2E_ORG_ID }}
         run: npx playwright test
       - name: Upload Playwright report
         uses: actions/upload-artifact@v4
diff --git a/packages/e2e/helpers/load-env.ts b/packages/e2e/helpers/load-env.ts
new file mode 100644
index 00000000000..4d749acafd2
--- /dev/null
+++ b/packages/e2e/helpers/load-env.ts
@@ -0,0 +1,30 @@
+/* eslint-disable no-restricted-imports */
+import * as fs from 'fs'
+import * as path from 'path'
+import {fileURLToPath} from 'url'
+
+/**
+ * Load a .env file into process.env (without overwriting existing values).
+ * Handles quotes and inline comments (e.g. "VALUE # comment" → "VALUE").
+ */
+export function loadEnv(dirOrUrl: string): void {
+  const dir = dirOrUrl.startsWith('file://') ? path.dirname(fileURLToPath(dirOrUrl)) : dirOrUrl
+  const envPath = path.join(dir, '.env')
+  if (!fs.existsSync(envPath)) return
+
+  for (const line of fs.readFileSync(envPath, 'utf-8').split('\n')) {
+    const trimmed = line.trim()
+    if (!trimmed || trimmed.startsWith('#')) continue
+    const eqIdx = trimmed.indexOf('=')
+    if (eqIdx === -1) continue
+    const key = trimmed.slice(0, eqIdx).trim()
+    let value = trimmed.slice(eqIdx + 1).trim()
+    if ((value.startsWith('"') && value.endsWith('"')) || (value.startsWith("'") && value.endsWith("'"))) {
+      value = value.slice(1, -1)
+    } else {
+      const commentIdx = value.indexOf(' #')
+      if (commentIdx !== -1) value = value.slice(0, commentIdx).trim()
+    }
+    process.env[key] ??= value
+  }
+}
diff --git a/packages/e2e/playwright.config.ts b/packages/e2e/playwright.config.ts
index f2260472c55..755b044fde6 100644
--- a/packages/e2e/playwright.config.ts
+++ b/packages/e2e/playwright.config.ts
@@ -1,25 +1,8 @@
 /* eslint-disable line-comment-position */
-/* eslint-disable no-restricted-imports */
+import {loadEnv} from './helpers/load-env.js'
 import {defineConfig} from '@playwright/test'
-import * as fs from 'fs'
-import * as path from 'path'
-import {fileURLToPath} from 'url'
 
-const __dirname = path.dirname(fileURLToPath(import.meta.url))
-
-// Load .env file if present (CI provides env vars directly)
-const envPath = path.join(__dirname, '.env')
-if (fs.existsSync(envPath)) {
-  for (const line of fs.readFileSync(envPath, 'utf-8').split('\n')) {
-    const trimmed = line.trim()
-    if (!trimmed || trimmed.startsWith('#')) continue
-    const eqIdx = trimmed.indexOf('=')
-    if (eqIdx === -1) continue
-    const key = trimmed.slice(0, eqIdx).trim()
-    const value = trimmed.slice(eqIdx + 1).trim()
-    process.env[key] ??= value
-  }
-}
+loadEnv(import.meta.url)
 
 const isCI = Boolean(process.env.CI)
 
diff --git a/packages/e2e/setup/app.ts b/packages/e2e/setup/app.ts
index dbd3da4b995..8b9d6cd5150 100644
--- a/packages/e2e/setup/app.ts
+++ b/packages/e2e/setup/app.ts
@@ -2,7 +2,7 @@
 import {authFixture} from './auth.js'
 import * as path from 'path'
 import * as fs from 'fs'
-import type {ExecResult} from './cli.js'
+import type {CLIProcess, ExecResult} from './cli.js'
 
 export interface AppScaffold {
   /** The directory where the app was created */
@@ -40,97 +40,124 @@ export interface AppInfoResult {
   }[]
 }
 
-/**
- * Test-scoped fixture that creates a fresh app in a temp directory.
- * Depends on authLogin (worker-scoped) for OAuth session.
- */
-export const appScaffoldFixture = authFixture.extend<{appScaffold: AppScaffold}>({
-  appScaffold: async ({cli, env, authLogin: _authLogin}, use) => {
-    const appTmpDir = fs.mkdtempSync(path.join(env.tempDir, 'app-'))
-    let appDir = ''
-
-    const scaffold: AppScaffold = {
-      get appDir() {
-        if (!appDir) throw new Error('App has not been initialized yet. Call init() first.')
-        return appDir
-      },
-
-      async init(opts: AppInitOptions) {
-        const name = opts.name ?? 'e2e-test-app'
-        const template = opts.template ?? 'reactRouter'
-        const packageManager = opts.packageManager ?? 'npm'
-
-        const args = [
-          '--name',
-          name,
-          '--path',
-          appTmpDir,
-          '--package-manager',
-          packageManager,
-          '--local',
-          '--template',
-          template,
-        ]
-        if (opts.flavor) args.push('--flavor', opts.flavor)
-
-        const result = await cli.execCreateApp(args, {
-          env: {FORCE_COLOR: '0'},
-          timeout: 5 * 60 * 1000,
-        })
-
-        const allOutput = `${result.stdout}\n${result.stderr}`
-        const match = allOutput.match(/([\w-]+) is ready for you to build!/)
-
-        if (match?.[1]) {
-          appDir = path.join(appTmpDir, match[1])
+/** Shared scaffold builder. defaultName is used when opts.name is omitted. */
+function buildScaffold(
+  cli: CLIProcess,
+  appTmpDir: string,
+  defaultName: string,
+  orgId?: string,
+): {scaffold: AppScaffold} {
+  let appDir = ''
+
+  const scaffold: AppScaffold = {
+    get appDir() {
+      if (!appDir) throw new Error('App has not been initialized yet. Call init() first.')
+      return appDir
+    },
+
+    async init(opts: AppInitOptions) {
+      const name = opts.name ?? defaultName
+      const template = opts.template ?? 'reactRouter'
+      const packageManager = opts.packageManager ?? 'npm'
+
+      const args = [
+        '--name',
+        name,
+        '--path',
+        appTmpDir,
+        '--package-manager',
+        packageManager,
+        '--local',
+        '--template',
+        template,
+      ]
+      if (orgId) args.push('--organization-id', orgId)
+      if (opts.flavor) args.push('--flavor', opts.flavor)
+
+      const result = await cli.execCreateApp(args, {
+        env: {FORCE_COLOR: '0'},
+        timeout: 5 * 60 * 1000,
+      })
+
+      if (result.exitCode !== 0) {
+        return result
+      }
+
+      const allOutput = `${result.stdout}\n${result.stderr}`
+      const match = allOutput.match(/([\w-]+) is ready for you to build!/)
+
+      if (match?.[1]) {
+        appDir = path.join(appTmpDir, match[1])
+      } else {
+        const entries = fs.readdirSync(appTmpDir, {withFileTypes: true})
+        const appEntry = entries.find(
+          (entry) => entry.isDirectory() && fs.existsSync(path.join(appTmpDir, entry.name, 'shopify.app.toml')),
+        )
+        if (appEntry) {
+          appDir = path.join(appTmpDir, appEntry.name)
         } else {
-          const entries = fs.readdirSync(appTmpDir, {withFileTypes: true})
-          const appEntry = entries.find(
-            (entry) => entry.isDirectory() && fs.existsSync(path.join(appTmpDir, entry.name, 'shopify.app.toml')),
+          throw new Error(
+            `Could not find created app directory in ${appTmpDir}.\n` +
+              `Exit code: ${result.exitCode}\nstdout: ${result.stdout}\nstderr: ${result.stderr}`,
           )
-          if (appEntry) {
-            appDir = path.join(appTmpDir, appEntry.name)
-          } else {
-            throw new Error(
-              `Could not find created app directory in ${appTmpDir}.\n` +
-                `Exit code: ${result.exitCode}\nstdout: ${result.stdout}\nstderr: ${result.stderr}`,
-            )
-          }
         }
+      }
 
-        const npmrcPath = path.join(appDir, '.npmrc')
-        if (!fs.existsSync(npmrcPath)) fs.writeFileSync(npmrcPath, '')
-        fs.appendFileSync(npmrcPath, 'frozen-lockfile=false\n')
+      const npmrcPath = path.join(appDir, '.npmrc')
+      if (!fs.existsSync(npmrcPath)) fs.writeFileSync(npmrcPath, '')
+      fs.appendFileSync(npmrcPath, 'frozen-lockfile=false\n')
 
-        return result
-      },
-
-      async generateExtension(opts: ExtensionOptions) {
-        const args = [
-          'app',
-          'generate',
-          'extension',
-          '--name',
-          opts.name,
-          '--path',
-          appDir,
-          '--template',
-          opts.template,
-        ]
-        if (opts.flavor) args.push('--flavor', opts.flavor)
-        return cli.exec(args, {timeout: 5 * 60 * 1000})
-      },
-
-      async build() {
-        return cli.exec(['app', 'build', '--path', appDir], {timeout: 5 * 60 * 1000})
-      },
-
-      async appInfo(): Promise<AppInfoResult> {
-        const result = await cli.exec(['app', 'info', '--path', appDir, '--json'])
-        return JSON.parse(result.stdout)
-      },
-    }
+      return result
+    },
+
+    async generateExtension(opts: ExtensionOptions) {
+      const args = ['app', 'generate', 'extension', '--name', opts.name, '--path', appDir, '--template', opts.template]
+      if (opts.flavor) args.push('--flavor', opts.flavor)
+      return cli.exec(args, {timeout: 5 * 60 * 1000})
+    },
 
+    async build() {
+      return cli.exec(['app', 'build', '--path', appDir], {timeout: 5 * 60 * 1000})
+    },
+
+    async appInfo(): Promise<AppInfoResult> {
+      const result = await cli.exec(['app', 'info', '--path', appDir, '--json'])
+      return JSON.parse(result.stdout)
+    },
+  }
+
+  return {scaffold}
+}
+
+/** Fixture: scaffolds a local app linked to a pre-existing remote app (via SHOPIFY_FLAG_CLIENT_ID). */
+export const appScaffoldFixture = authFixture.extend<{appScaffold: AppScaffold}>({
+  appScaffold: async ({cli, env, authLogin: _authLogin}, use) => {
+    const appTmpDir = fs.mkdtempSync(path.join(env.tempDir, 'app-'))
+    const {scaffold} = buildScaffold(cli, appTmpDir, 'e2e-test-app')
+    await use(scaffold)
+    fs.rmSync(appTmpDir, {recursive: true, force: true})
+  },
+})
+
+/** CLI wrapper that strips SHOPIFY_FLAG_CLIENT_ID so commands use the toml's client_id. */
+function makeFreshCli(baseCli: CLIProcess, baseProcessEnv: NodeJS.ProcessEnv): CLIProcess {
+  const freshEnv = {...baseProcessEnv, SHOPIFY_FLAG_CLIENT_ID: undefined}
+  return {
+    exec: (args, opts = {}) => baseCli.exec(args, {...opts, env: {...freshEnv, ...opts.env}}),
+    execCreateApp: (args, opts = {}) => baseCli.execCreateApp(args, {...opts, env: {...freshEnv, ...opts.env}}),
+    spawn: (args, opts = {}) => baseCli.spawn(args, {...opts, env: {...freshEnv, ...opts.env}}),
+  }
+}
+
+/** Fixture: creates a brand-new app on every run. Requires E2E_ORG_ID. */
+export const freshAppScaffoldFixture = authFixture.extend<{appScaffold: AppScaffold; cli: CLIProcess}>({
+  cli: async ({cli: baseCli, env}, use) => {
+    await use(makeFreshCli(baseCli, env.processEnv))
+  },
+
+  appScaffold: async ({cli, env, authLogin: _authLogin}, use) => {
+    const appTmpDir = fs.mkdtempSync(path.join(env.tempDir, 'fresh-app-'))
+    const {scaffold} = buildScaffold(cli, appTmpDir, `QA-E2E-1st-${Date.now()}`, env.orgId || undefined)
     await use(scaffold)
     fs.rmSync(appTmpDir, {recursive: true, force: true})
   },
diff --git a/packages/e2e/setup/auth.ts b/packages/e2e/setup/auth.ts
index 93f224c1844..8b049474b41 100644
--- a/packages/e2e/setup/auth.ts
+++ b/packages/e2e/setup/auth.ts
@@ -36,8 +36,7 @@ export const authFixture = cliFixture.extend<{}, {authLogin: void}>({
         if (value !== undefined) spawnEnv[key] = value
       }
       spawnEnv.CI = ''
-      // Pretend we're in a cloud environment so the CLI prints the login URL
-      // directly instead of opening a system browser (BROWSER=none doesn't work on macOS)
+      // Print login URL directly instead of opening system browser
       spawnEnv.CODESPACES = 'true'
 
       const ptyProcess = nodePty.spawn('node', [executables.cli, 'auth', 'login'], {
@@ -83,8 +82,7 @@ export const authFixture = cliFixture.extend<{}, {authLogin: void}>({
         // Process may already be dead
       }
 
-      // Remove the partners token so CLI uses the OAuth session
-      // instead of the token (which can't auth against Business Platform API)
+      // Drop token so CLI uses the OAuth session instead
       delete env.processEnv.SHOPIFY_CLI_PARTNERS_TOKEN
 
       await use()
diff --git a/packages/e2e/setup/cli.ts b/packages/e2e/setup/cli.ts
index f3e178abaea..9f84f9eeb64 100644
--- a/packages/e2e/setup/cli.ts
+++ b/packages/e2e/setup/cli.ts
@@ -45,19 +45,22 @@ export const cliFixture = envFixture.extend<{cli: CLIProcess}>({
   cli: async ({env}, use) => {
     const spawnedProcesses: SpawnedProcess[] = []
 
+    // Merge env with opts, filtering out undefined values
+    function buildEnv(optsEnv?: Record<string, string | undefined>): {[key: string]: string} {
+      const result: {[key: string]: string} = {}
+      for (const [key, value] of Object.entries({...env.processEnv, ...optsEnv})) {
+        if (value !== undefined) result[key] = value
+      }
+      return result
+    }
+
     const cli: CLIProcess = {
       async exec(args, opts = {}) {
         // 3 min default
         const timeout = opts.timeout ?? 3 * 60 * 1000
-        const execEnv: {[key: string]: string} = {}
-        for (const [key, value] of Object.entries({...env.processEnv, ...opts.env})) {
-          if (value !== undefined) {
-            execEnv[key] = value
-          }
-        }
         const execaOpts: ExecaOptions = {
           cwd: opts.cwd,
-          env: execEnv,
+          env: buildEnv(opts.env),
           extendEnv: false,
           timeout,
           reject: false,
@@ -79,15 +82,9 @@ export const cliFixture = envFixture.extend<{cli: CLIProcess}>({
       async execCreateApp(args, opts = {}) {
         // 5 min default for scaffolding
         const timeout = opts.timeout ?? 5 * 60 * 1000
-        const execEnv: {[key: string]: string} = {}
-        for (const [key, value] of Object.entries({...env.processEnv, ...opts.env})) {
-          if (value !== undefined) {
-            execEnv[key] = value
-          }
-        }
         const execaOpts: ExecaOptions = {
           cwd: opts.cwd,
-          env: execEnv,
+          env: buildEnv(opts.env),
           extendEnv: false,
           timeout,
           reject: false,
@@ -99,6 +96,11 @@ export const cliFixture = envFixture.extend<{cli: CLIProcess}>({
 
         const result = await execa('node', [executables.createApp, ...args], execaOpts)
 
+        if (process.env.DEBUG === '1') {
+          if (result.stdout) console.log(`[e2e] execCreateApp stdout:\n${result.stdout}`)
+          if (result.stderr) console.log(`[e2e] execCreateApp stderr:\n${result.stderr}`)
+        }
+
         return {
           stdout: result.stdout ?? '',
           stderr: result.stderr ?? '',
@@ -110,13 +112,6 @@ export const cliFixture = envFixture.extend<{cli: CLIProcess}>({
         // Dynamic import to avoid requiring node-pty for Phase 1 tests
         const nodePty = await import('node-pty')
 
-        const spawnEnv: {[key: string]: string} = {}
-        for (const [key, value] of Object.entries({...env.processEnv, ...opts.env})) {
-          if (value !== undefined) {
-            spawnEnv[key] = value
-          }
-        }
-
         if (process.env.DEBUG === '1') {
           console.log(`[e2e] spawn: node ${executables.cli} ${args.join(' ')}`)
         }
@@ -126,7 +121,7 @@ export const cliFixture = envFixture.extend<{cli: CLIProcess}>({
           cols: 120,
           rows: 30,
           cwd: opts.cwd,
-          env: spawnEnv,
+          env: buildEnv(opts.env),
         })
 
         let output = ''
diff --git a/packages/e2e/setup/env.ts b/packages/e2e/setup/env.ts
index ea22c69ceb6..02e0f0f718f 100644
--- a/packages/e2e/setup/env.ts
+++ b/packages/e2e/setup/env.ts
@@ -16,6 +16,8 @@ export interface E2EEnv {
   storeFqdn: string
   /** Secondary app client ID for config link tests */
   secondaryClientId: string
+  /** Dedicated e2e Partners org ID for fresh-app tests (empty string if not set) */
+  orgId: string
   /** Environment variables to pass to CLI processes */
   processEnv: NodeJS.ProcessEnv
   /** Temporary directory root for this worker */
@@ -66,7 +68,7 @@ export function createIsolatedEnv(baseDir: string): {tempDir: string; xdgEnv: {[
  */
 export function requireEnv(
   env: E2EEnv,
-  ...keys: (keyof Pick<E2EEnv, 'partnersToken' | 'clientId' | 'storeFqdn' | 'secondaryClientId'>)[]
+  ...keys: (keyof Pick<E2EEnv, 'partnersToken' | 'clientId' | 'storeFqdn' | 'secondaryClientId' | 'orgId'>)[]
 ): void {
   for (const key of keys) {
     if (!env[key]) {
@@ -75,6 +77,7 @@ export function requireEnv(
         clientId: 'SHOPIFY_FLAG_CLIENT_ID',
         storeFqdn: 'E2E_STORE_FQDN',
         secondaryClientId: 'E2E_SECONDARY_CLIENT_ID',
+        orgId: 'E2E_ORG_ID',
       }
       throw new Error(`${envVarNames[key]} environment variable is required for this test`)
     }
@@ -93,6 +96,7 @@ export const envFixture = base.extend<{}, {env: E2EEnv}>({
       const clientId = process.env.SHOPIFY_FLAG_CLIENT_ID ?? ''
       const storeFqdn = process.env.E2E_STORE_FQDN ?? ''
       const secondaryClientId = process.env.E2E_SECONDARY_CLIENT_ID ?? ''
+      const orgId = process.env.E2E_ORG_ID ?? ''
 
       const tmpBase = process.env.E2E_TEMP_DIR ?? path.join(directories.root, '.e2e-tmp')
       fs.mkdirSync(tmpBase, {recursive: true})
@@ -104,8 +108,8 @@ export const envFixture = base.extend<{}, {env: E2EEnv}>({
         ...xdgEnv,
         SHOPIFY_RUN_AS_USER: '0',
         NODE_OPTIONS: '',
-        // Prevent interactive prompts
         CI: '1',
+        SHOPIFY_CLI_1P_DEV: undefined,
       }
 
       if (partnersToken) {
@@ -123,13 +127,14 @@ export const envFixture = base.extend<{}, {env: E2EEnv}>({
         clientId,
         storeFqdn,
         secondaryClientId,
+        orgId,
         processEnv,
         tempDir,
       }
 
       await use(env)
 
-      // Cleanup: remove temp directory
+      // Cleanup
       fs.rmSync(tempDir, {recursive: true, force: true})
     },
     {scope: 'worker'},
diff --git a/packages/e2e/tests/app-basic.spec.ts b/packages/e2e/tests/app-basic.spec.ts
index 0ca04eb118d..21589a15942 100644
--- a/packages/e2e/tests/app-basic.spec.ts
+++ b/packages/e2e/tests/app-basic.spec.ts
@@ -11,12 +11,10 @@ test.describe('App basic flow (no extensions)', () => {
     cli,
     env,
   }) => {
-    // Full flow: init + dev (3 min) + deploy + config link + secondary deploy — needs 10 min
     test.setTimeout(10 * 60 * 1000)
-
     requireEnv(env, 'clientId', 'storeFqdn', 'secondaryClientId')
 
-    // Step 1: Create a React Router app
+    // Step 1: Scaffold app (links to pre-existing app via SHOPIFY_FLAG_CLIENT_ID)
     const initResult = await appScaffold.init({
       template: 'reactRouter',
       flavor: 'javascript',
@@ -24,15 +22,14 @@ test.describe('App basic flow (no extensions)', () => {
     })
     expect(initResult.exitCode, '‼️ Step 1 - app init failed').toBe(0)
 
-    // Step 2: Start dev server via PTY
-    // Unset CI so keyboard shortcuts are enabled in the Dev UI
+    // Step 2: Start dev server (CI='' enables keyboard shortcuts)
     const dev = await cli.spawn(['app', 'dev', '--path', appScaffold.appDir], {env: {CI: ''}})
     try {
       await dev.waitForOutput('Ready, watching for changes in your app', 3 * 60 * 1000).catch((err: Error) => {
         throw new Error(`‼️ Step 2 - app dev failed\n${err.message}`)
       })
 
-      // Step 3: Run a GraphQL query while the dev server is running
+      // Step 3: Run a GraphQL query
       const executeResult = await cli.exec(
         ['app', 'execute', '--query', 'query { shop { name } }', '--path', appScaffold.appDir],
         {timeout: 60 * 1000},
@@ -41,14 +38,14 @@ test.describe('App basic flow (no extensions)', () => {
       expect(executeResult.exitCode, '‼️ Step 3 - app execute failed').toBe(0)
       expect(executeOutput, '‼️ Step 3 - app execute: response missing "shop" field').toContain('"shop"')
 
-      // Step 4: Press q to quit the dev server
+      // Step 4: Quit dev server
       dev.sendKey('q')
       const devExitCode = await dev.waitForExit(30_000).catch((err: Error) => {
         throw new Error(`‼️ Step 4 - app dev did not exit after pressing q\n${err.message}`)
       })
       expect(devExitCode, '‼️ Step 4 - app dev quit failed').toBe(0)
     } finally {
-      // Step 5: Always clean up the dev preview, even if the test fails
+      // Step 5: Clean up dev preview (runs even if test fails)
       dev.kill()
       const cleanResult = await cli.exec(['app', 'dev', 'clean', '--path', appScaffold.appDir])
       const cleanOutput = cleanResult.stdout + cleanResult.stderr
@@ -58,7 +55,7 @@ test.describe('App basic flow (no extensions)', () => {
       )
     }
 
-    // Step 6: Deploy the primary app
+    // Step 6: Deploy
     const versionTag = `QA-E2E-1st-${Date.now()}`
     const deployResult = await cli.exec(
       [
@@ -76,7 +73,7 @@ test.describe('App basic flow (no extensions)', () => {
     )
     expect(deployResult.exitCode, '‼️ Step 6 - app deploy failed').toBe(0)
 
-    // Step 7: List versions and verify our tag appears
+    // Step 7: Verify version appears in list
     const listResult = await cli.exec(['app', 'versions', 'list', '--path', appScaffold.appDir, '--json'], {
       timeout: 60 * 1000,
     })
@@ -84,13 +81,8 @@ test.describe('App basic flow (no extensions)', () => {
     expect(listResult.exitCode, '‼️ Step 7 - app versions list failed').toBe(0)
     expect(listOutput, `‼️ Step 7 - app versions list: missing version tag "${versionTag}"`).toContain(versionTag)
 
-    // Step 8: Config link to the secondary app
-    // Pre-create a minimal TOML stub so getTomls() finds the secondary client ID and skips
-    // the interactive "Configuration file name" prompt entirely. This avoids PTY timing races
-    // where the Enter key arrives before ink has fully initialized the text prompt, which
-    // causes renderTextPrompt to return '' → filenameFromName('') = 'shopify.app.toml' →
-    // that file already exists → overwrite confirmation prompt hangs.
-    // (--config and --client-id are mutually exclusive flags, so we can't pass both directly.)
+    // Step 8: Config link to secondary app
+    // TOML stub so config link skips the "Configuration file name" prompt
     fs.writeFileSync(
       path.join(appScaffold.appDir, 'shopify.app.secondary.toml'),
       `client_id = "${env.secondaryClientId}"\n`,
@@ -106,7 +98,7 @@ test.describe('App basic flow (no extensions)', () => {
     const configLinkExitCode = await configLink.waitForExit(30_000)
     expect(configLinkExitCode, '‼️ Step 8 - app config link failed').toBe(0)
 
-    // Step 9: Deploy to the secondary app using the linked config file
+    // Step 9: Deploy to secondary app
     const secondaryVersionTag = `QA-E2E-2nd-${Date.now()}`
     const secondaryDeployResult = await cli.exec(
       [
diff --git a/packages/e2e/tests/app-from-scratch.spec.ts b/packages/e2e/tests/app-from-scratch.spec.ts
new file mode 100644
index 00000000000..e57945d68bc
--- /dev/null
+++ b/packages/e2e/tests/app-from-scratch.spec.ts
@@ -0,0 +1,167 @@
+import {freshAppScaffoldFixture as test} from '../setup/app.js'
+import {requireEnv} from '../setup/env.js'
+import {expect} from '@playwright/test'
+import * as fs from 'fs'
+import * as path from 'path' // eslint-disable-line no-restricted-imports
+
+test.describe('App basic flow — from scratch', () => {
+  test('init, dev, execute, quit, clean, deploy, versions, config link, deploy to secondary', async ({
+    appScaffold,
+    cli,
+    env,
+  }) => {
+    test.setTimeout(15 * 60 * 1000)
+    requireEnv(env, 'storeFqdn', 'orgId')
+
+    // Step 1: Create a new app (non-interactive via --organization-id + --name)
+    const initResult = await appScaffold.init({
+      template: 'reactRouter',
+      flavor: 'typescript',
+      packageManager: 'npm',
+    })
+    expect(initResult.exitCode, '‼️ Step 1 - app init failed').toBe(0)
+
+    // Step 2: Start dev server (CI='' enables keyboard shortcuts)
+    const dev = await cli.spawn(['app', 'dev', '--path', appScaffold.appDir], {env: {CI: ''}})
+    try {
+      await dev.waitForOutput('Ready, watching for changes in your app', 3 * 60 * 1000).catch((err: Error) => {
+        throw new Error(`‼️ Step 2 - app dev failed\n${err.message}`)
+      })
+
+      // Step 3: Run a GraphQL query
+      const executeResult = await cli.exec(
+        ['app', 'execute', '--query', 'query { shop { name } }', '--path', appScaffold.appDir],
+        {timeout: 60 * 1000},
+      )
+      const executeOutput = executeResult.stdout + executeResult.stderr
+      expect(executeResult.exitCode, '‼️ Step 3 - app execute failed').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).catch((err: Error) => {
+        throw new Error(`‼️ Step 4 - app dev did not exit after pressing q\n${err.message}`)
+      })
+      expect(devExitCode, '‼️ Step 4 - app dev quit failed').toBe(0)
+    } finally {
+      // Step 5: Clean up dev preview (runs even if test fails)
+      dev.kill()
+      const cleanResult = await cli.exec(['app', 'dev', 'clean', '--path', appScaffold.appDir])
+      const cleanOutput = cleanResult.stdout + cleanResult.stderr
+      expect(cleanResult.exitCode, '‼️ Step 5 - app dev clean failed').toBe(0)
+      expect(cleanOutput, '‼️ Step 5 - app dev clean: missing "Dev preview stopped" in output').toContain(
+        'Dev preview stopped',
+      )
+    }
+
+    // Step 6: Deploy
+    const versionTag = `QA-E2E-1st-${Date.now()}`
+    const deployResult = await cli.exec(
+      [
+        'app',
+        'deploy',
+        '--path',
+        appScaffold.appDir,
+        '--force',
+        '--version',
+        versionTag,
+        '--message',
+        'E2E basic flow deployment',
+      ],
+      {timeout: 5 * 60 * 1000},
+    )
+    expect(deployResult.exitCode, '‼️ Step 6 - app deploy failed').toBe(0)
+
+    // Step 7: Verify version appears in list
+    const listResult = await cli.exec(['app', 'versions', 'list', '--path', appScaffold.appDir, '--json'], {
+      timeout: 60 * 1000,
+    })
+    const listOutput = listResult.stdout + listResult.stderr
+    expect(listResult.exitCode, '‼️ Step 7 - app versions list failed').toBe(0)
+    expect(listOutput, `‼️ Step 7 - app versions list: missing version tag "${versionTag}"`).toContain(versionTag)
+
+    // Step 8: Create a second app, then config link to it
+    const secondaryAppName = `QA-E2E-2nd-${Date.now()}`
+    const secondaryTmpDir = fs.mkdtempSync(path.join(appScaffold.appDir, '..', 'secondary-'))
+    const secondaryInitResult = await cli.execCreateApp(
+      [
+        '--name',
+        secondaryAppName,
+        '--path',
+        secondaryTmpDir,
+        '--package-manager',
+        'npm',
+        '--local',
+        '--template',
+        'reactRouter',
+        '--flavor',
+        'typescript',
+        '--organization-id',
+        env.orgId,
+      ],
+      {env: {FORCE_COLOR: '0'}, timeout: 5 * 60 * 1000},
+    )
+    expect(secondaryInitResult.exitCode, '‼️ Step 8a - secondary app init failed').toBe(0)
+
+    // Read client_id from the new app's toml
+    const secondaryAppDir = fs
+      .readdirSync(secondaryTmpDir, {withFileTypes: true})
+      .find((entry) => entry.isDirectory() && fs.existsSync(path.join(secondaryTmpDir, entry.name, 'shopify.app.toml')))
+    expect(secondaryAppDir, '‼️ Step 8a - secondary app dir not found').toBeTruthy()
+    const secondaryToml = fs.readFileSync(
+      path.join(secondaryTmpDir, secondaryAppDir!.name, 'shopify.app.toml'),
+      'utf-8',
+    )
+    const clientIdMatch = secondaryToml.match(/client_id\s*=\s*"([^"]+)"/)
+    expect(clientIdMatch, '‼️ Step 8a - client_id not found in secondary toml').toBeTruthy()
+    const secondaryClientId = clientIdMatch![1]!
+
+    // TOML stub so config link skips the "Configuration file name" prompt
+    fs.writeFileSync(
+      path.join(appScaffold.appDir, 'shopify.app.secondary.toml'),
+      `client_id = "${secondaryClientId}"\n`,
+    )
+
+    // Link to the secondary app
+    const configLinkResult = await cli.exec(
+      ['app', 'config', 'link', '--path', appScaffold.appDir, '--client-id', secondaryClientId],
+      {timeout: 2 * 60 * 1000},
+    )
+    expect(
+      configLinkResult.exitCode,
+      `‼️ Step 8b - app config link failed\nstdout: ${configLinkResult.stdout}\nstderr: ${configLinkResult.stderr}`,
+    ).toBe(0)
+    const configLinkOutput = configLinkResult.stdout + configLinkResult.stderr
+    expect(configLinkOutput, '‼️ Step 8b - config link: missing "is now linked" in output').toContain(
+      'is now linked to',
+    )
+
+    fs.rmSync(secondaryTmpDir, {recursive: true, force: true})
+
+    // Step 9: Deploy to the secondary app
+    const tomlFiles = fs
+      .readdirSync(appScaffold.appDir)
+      .filter(
+        (file: string) => file.startsWith('shopify.app.') && file.endsWith('.toml') && file !== 'shopify.app.toml',
+      )
+    const secondaryConfig = tomlFiles[0]?.replace('shopify.app.', '').replace('.toml', '') ?? 'secondary'
+    const secondaryVersionTag = `QA-E2E-2nd-${Date.now()}`
+    const secondaryDeployResult = await cli.exec(
+      [
+        'app',
+        'deploy',
+        '--path',
+        appScaffold.appDir,
+        '--config',
+        secondaryConfig,
+        '--force',
+        '--version',
+        secondaryVersionTag,
+        '--message',
+        'E2E secondary app deployment',
+      ],
+      {timeout: 5 * 60 * 1000},
+    )
+    expect(secondaryDeployResult.exitCode, '‼️ Step 9 - app deploy (secondary) failed').toBe(0)
+  })
+})