diff --git a/packages/app/src/cli/services/init/init.test.ts b/packages/app/src/cli/services/init/init.test.ts
new file mode 100644
index 00000000000..70dcde26cfe
--- /dev/null
+++ b/packages/app/src/cli/services/init/init.test.ts
@@ -0,0 +1,27 @@
+import {ensurePnpmWorkspaceFile} from './init.js'
+import {describe, expect, test} from 'vitest'
+import {inTemporaryDirectory, writeFile, readFile} from '@shopify/cli-kit/node/fs'
+import {joinPath} from '@shopify/cli-kit/node/path'
+
+describe('ensurePnpmWorkspaceFile', () => {
+  test('generates file when template has none', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      await ensurePnpmWorkspaceFile(tmpDir, ['extensions/*'])
+
+      const content = await readFile(joinPath(tmpDir, 'pnpm-workspace.yaml'))
+      expect(content).toBe("packages:\n - 'extensions/*'")
+    })
+  })
+
+  test('does not overwrite existing file from template', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      const templateContent = `packages:\n  - 'extensions/*'\nallowBuilds:\n  esbuild: true\n`
+      await writeFile(joinPath(tmpDir, 'pnpm-workspace.yaml'), templateContent)
+
+      await ensurePnpmWorkspaceFile(tmpDir, ['extensions/*'])
+
+      const content = await readFile(joinPath(tmpDir, 'pnpm-workspace.yaml'))
+      expect(content).toBe(templateContent)
+    })
+  })
+})
diff --git a/packages/app/src/cli/services/init/init.ts b/packages/app/src/cli/services/init/init.ts
index 74be02232c7..e4d0cc9e34b 100644
--- a/packages/app/src/cli/services/init/init.ts
+++ b/packages/app/src/cli/services/init/init.ts
@@ -117,8 +117,7 @@ async function init(options: InitOptions) {
               packageJSON.workspaces = workspacesFolders
               break
             case 'pnpm': {
-              const workspacesContent = workspacesFolders.map((folder) => ` - '${folder}'`).join(`\n`)
-              await writeFile(joinPath(templateScaffoldDir, 'pnpm-workspace.yaml'), `packages:\n${workspacesContent}`)
+              await ensurePnpmWorkspaceFile(templateScaffoldDir, workspacesFolders)
               // Ensure that the installation of dependencies doesn't fail when using
               // pnpm due to missing peerDependencies.
               await appendFile(joinPath(templateScaffoldDir, '.npmrc'), `auto-install-peers=true\n`)
@@ -273,4 +272,13 @@ function detectAdditionalWorkspacesFolders(directory: string) {
   return ['web', 'web/frontend'].filter((folder) => fileExistsSync(joinPath(directory, folder)))
 }
 
+export async function ensurePnpmWorkspaceFile(directory: string, workspacesFolders: string[]) {
+  const pnpmWorkspacePath = joinPath(directory, 'pnpm-workspace.yaml')
+  if (await fileExists(pnpmWorkspacePath)) {
+    return
+  }
+  const workspacesContent = workspacesFolders.map((folder) => ` - '${folder}'`).join(`\n`)
+  await writeFile(pnpmWorkspacePath, `packages:\n${workspacesContent}`)
+}
+
 export default init