diff --git a/.changeset/silver-mice-thank.md b/.changeset/silver-mice-thank.md
new file mode 100644
index 00000000000..3cb763c622f
--- /dev/null
+++ b/.changeset/silver-mice-thank.md
@@ -0,0 +1,6 @@
+---
+'@shopify/cli-kit': patch
+'@shopify/app': patch
+---
+
+Remove all template lockfiles, except the one used to install dependencies
diff --git a/packages/app/src/cli/services/init/init.ts b/packages/app/src/cli/services/init/init.ts
index 6cdfa3417f9..1a3e2659585 100644
--- a/packages/app/src/cli/services/init/init.ts
+++ b/packages/app/src/cli/services/init/init.ts
@@ -180,7 +180,7 @@ async function init(options: InitOptions) {
       {
         title: 'Cleaning up',
         task: async () => {
-          await cleanup(templateScaffoldDir)
+          await cleanup(templateScaffoldDir, packageManager)
         },
       },
       {
diff --git a/packages/app/src/cli/services/init/template/cleanup.test.ts b/packages/app/src/cli/services/init/template/cleanup.test.ts
index 51a4240c06c..37fe613d02e 100644
--- a/packages/app/src/cli/services/init/template/cleanup.test.ts
+++ b/packages/app/src/cli/services/init/template/cleanup.test.ts
@@ -2,6 +2,7 @@ import cleanup from './cleanup.js'
 import {describe, expect, test} from 'vitest'
 import {inTemporaryDirectory, mkdir, writeFile, fileExists} from '@shopify/cli-kit/node/fs'
 import {joinPath} from '@shopify/cli-kit/node/path'
+import {PackageManager} from '@shopify/cli-kit/node/node-package-manager'
 
 describe('cleanup', () => {
   async function mockProjectFolder(tmpDir: string) {
@@ -35,7 +36,7 @@ describe('cleanup', () => {
       await mockProjectFolder(tmpDir)
 
       // When
-      await cleanup(tmpDir)
+      await cleanup(tmpDir, 'npm')
 
       // Then
       await expect(fileExists(joinPath(tmpDir, '.git'))).resolves.toBe(false)
@@ -52,7 +53,7 @@ describe('cleanup', () => {
       await mockProjectFolder(tmpDir)
 
       // When
-      await cleanup(tmpDir)
+      await cleanup(tmpDir, 'npm')
 
       // Then
       await expect(fileExists(joinPath(tmpDir, 'server.js'))).resolves.toBe(true)
@@ -60,4 +61,42 @@ describe('cleanup', () => {
       await expect(fileExists(joinPath(tmpDir, 'frontend', 'node_modules'))).resolves.toBe(true)
     })
   })
+
+  test.each(['npm', 'yarn', 'pnpm', 'bun'])('deletes unused lockfiles for %s', async (packageManager) => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      await mockProjectFolder(tmpDir)
+      await writeFile(joinPath(tmpDir, 'package-lock.json'), '{}')
+      await writeFile(joinPath(tmpDir, 'yarn.lock'), '{}')
+      await writeFile(joinPath(tmpDir, 'pnpm-lock.yaml'), '{}')
+      await writeFile(joinPath(tmpDir, 'bun.lockb'), '{}')
+
+      // When
+      await cleanup(tmpDir, packageManager as PackageManager)
+
+      // Then
+      await expect(fileExists(joinPath(tmpDir, 'package-lock.json'))).resolves.toBe(packageManager === 'npm')
+      await expect(fileExists(joinPath(tmpDir, 'yarn.lock'))).resolves.toBe(packageManager === 'yarn')
+      await expect(fileExists(joinPath(tmpDir, 'pnpm-lock.yaml'))).resolves.toBe(packageManager === 'pnpm')
+      await expect(fileExists(joinPath(tmpDir, 'bun.lockb'))).resolves.toBe(packageManager === 'bun')
+    })
+  })
+
+  test('deletes all lockfiles for unknown package manager', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      await mockProjectFolder(tmpDir)
+      await writeFile(joinPath(tmpDir, 'package-lock.json'), '{}')
+      await writeFile(joinPath(tmpDir, 'yarn.lock'), '{}')
+      await writeFile(joinPath(tmpDir, 'pnpm-lock.yaml'), '{}')
+      await writeFile(joinPath(tmpDir, 'bun.lockb'), '{}')
+
+      // When
+      await cleanup(tmpDir, 'unknown')
+
+      // Then
+      await expect(fileExists(joinPath(tmpDir, 'package-lock.json'))).resolves.toBe(false)
+      await expect(fileExists(joinPath(tmpDir, 'yarn.lock'))).resolves.toBe(false)
+      await expect(fileExists(joinPath(tmpDir, 'pnpm-lock.yaml'))).resolves.toBe(false)
+      await expect(fileExists(joinPath(tmpDir, 'bun.lockb'))).resolves.toBe(false)
+    })
+  })
 })
diff --git a/packages/app/src/cli/services/init/template/cleanup.ts b/packages/app/src/cli/services/init/template/cleanup.ts
index fa46e90b370..fde535065e4 100644
--- a/packages/app/src/cli/services/init/template/cleanup.ts
+++ b/packages/app/src/cli/services/init/template/cleanup.ts
@@ -1,7 +1,8 @@
-import {rmdir, glob} from '@shopify/cli-kit/node/fs'
+import {rmdir, glob, fileExistsSync, unlinkFile} from '@shopify/cli-kit/node/fs'
+import {Lockfile, lockfilesByManager, PackageManager} from '@shopify/cli-kit/node/node-package-manager'
 import {joinPath} from '@shopify/cli-kit/node/path'
 
-export default async function cleanup(webOutputDirectory: string) {
+export default async function cleanup(webOutputDirectory: string, packageManager: PackageManager) {
   const gitPaths = await glob(
     [
       joinPath(webOutputDirectory, '**', '.git'),
@@ -20,5 +21,14 @@ export default async function cleanup(webOutputDirectory: string) {
     },
   )
 
-  return Promise.all(gitPaths.map((path) => rmdir(path, {force: true}))).then(() => {})
+  const gitPathPromises = gitPaths.map((path) => rmdir(path, {force: true}))
+
+  const lockfilePromises = Object.entries(lockfilesByManager)
+    .filter(([manager, lockfile]) => manager !== packageManager && lockfile)
+    .map(([_, lockfile]) => {
+      const path = joinPath(webOutputDirectory, lockfile as Lockfile)
+      if (fileExistsSync(path)) return unlinkFile(path)
+    }, [])
+
+  return Promise.all([...gitPathPromises, ...lockfilePromises])
 }
diff --git a/packages/cli-kit/src/public/node/fs.ts b/packages/cli-kit/src/public/node/fs.ts
index 44799515c9f..b9ee1291900 100644
--- a/packages/cli-kit/src/public/node/fs.ts
+++ b/packages/cli-kit/src/public/node/fs.ts
@@ -43,6 +43,7 @@ import {
   chmod as fsChmod,
   access as fsAccess,
   rename as fsRename,
+  unlink as fsUnlink,
 } from 'fs/promises'
 import {pathToFileURL as pathToFile} from 'url'
 import * as os from 'os'
@@ -329,14 +330,24 @@ export function fileSizeSync(path: string): number {
 }
 
 /**
- * Unlink a file at the given path.
+ * Synchronously unlink a file at the given path.
+ *
  * @param path - Path to the file.
- * @returns A promise that resolves when the file is unlinked.
  */
 export function unlinkFileSync(path: string): void {
   fsUnlinkSync(path)
 }
 
+/**
+ * Unlink a file at the given path.
+ *
+ * @param path - Path to the file.
+ * @returns A promise that resolves when the file is unlinked.
+ */
+export function unlinkFile(path: string): Promise<void> {
+  return fsUnlink(path)
+}
+
 /**
  * Create a read stream for a file with optional options.
  *
diff --git a/packages/cli-kit/src/public/node/node-package-manager.ts b/packages/cli-kit/src/public/node/node-package-manager.ts
index 99094948dd1..89dcb0ca417 100644
--- a/packages/cli-kit/src/public/node/node-package-manager.ts
+++ b/packages/cli-kit/src/public/node/node-package-manager.ts
@@ -29,6 +29,13 @@ export const pnpmWorkspaceFile = 'pnpm-workspace.yaml'
 
 /** An array containing the lockfiles from all the package managers */
 export const lockfiles: Lockfile[] = [yarnLockfile, pnpmLockfile, npmLockfile, bunLockfile]
+export const lockfilesByManager: {[key in PackageManager]: Lockfile | undefined} = {
+  yarn: yarnLockfile,
+  npm: npmLockfile,
+  pnpm: pnpmLockfile,
+  bun: bunLockfile,
+  unknown: undefined,
+}
 export type Lockfile = 'yarn.lock' | 'package-lock.json' | 'pnpm-lock.yaml' | 'bun.lockb'
 
 /**