diff --git a/.changeset/silly-teachers-cry.md b/.changeset/silly-teachers-cry.md
new file mode 100644
index 0000000000..5a63386809
--- /dev/null
+++ b/.changeset/silly-teachers-cry.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/package-store": patch
+---
+
+`pnpm store prune` should not fail if the store directory doesn't exist.
diff --git a/store/package-store/src/storeController/prune.ts b/store/package-store/src/storeController/prune.ts
index 00a657dfb9..58d18f4c38 100644
--- a/store/package-store/src/storeController/prune.ts
+++ b/store/package-store/src/storeController/prune.ts
@@ -1,4 +1,5 @@
-import { promises as fs } from 'fs'
+import { type Dirent, promises as fs } from 'fs'
+import util from 'util'
 import path from 'path'
 import { type PackageFilesIndex } from '@pnpm/store.cafs'
 import { globalInfo, globalWarn } from '@pnpm/logger'
@@ -24,9 +25,7 @@ export async function prune ({ cacheDir, storeDir }: PruneOptions, removeAlienFi
   globalInfo('Removed all cached metadata files')
   const pkgIndexFiles = [] as string[]
   const removedHashes = new Set<string>()
-  const dirs = (await fs.readdir(cafsDir, { withFileTypes: true }))
-    .filter(entry => entry.isDirectory())
-    .map(dir => dir.name)
+  const dirs = await getSubdirsSafely(cafsDir)
   let fileCounter = 0
   await Promise.all(dirs.map(async (dir) => {
     const subdir = path.join(cafsDir, dir)
@@ -67,3 +66,18 @@ export async function prune ({ cacheDir, storeDir }: PruneOptions, removeAlienFi
   }))
   globalInfo(`Removed ${pkgCounter} package${pkgCounter === 1 ? '' : 's'}`)
 }
+
+async function getSubdirsSafely (dir: string): Promise<string[]> {
+  let entries: Dirent[]
+  try {
+    entries = await fs.readdir(dir, { withFileTypes: true }) as Dirent[]
+  } catch (err: unknown) {
+    if (util.types.isNativeError(err) && 'code' in err && err.code === 'ENOENT') {
+      return []
+    }
+    throw err
+  }
+  return entries
+    .filter(entry => entry.isDirectory())
+    .map(dir => dir.name)
+}
diff --git a/store/plugin-commands-store/test/storePrune.ts b/store/plugin-commands-store/test/storePrune.ts
index b19cbddb5f..8402da1b70 100644
--- a/store/plugin-commands-store/test/storePrune.ts
+++ b/store/plugin-commands-store/test/storePrune.ts
@@ -281,6 +281,67 @@ test('prune removes alien files from the store if the --force flag is used', asy
   expect(fs.existsSync(alienDir)).toBeFalsy()
 })
 
+describe('prune when store directory is not properly configured', () => {
+  test('prune will not fail if the store directory does not exist (ENOENT)', async () => {
+    prepareEmpty()
+    const nonExistentStoreDir = path.resolve('store')
+    const reporter = jest.fn()
+
+    await expect(
+      store.handler({
+        cacheDir: path.resolve('cache'),
+        dir: process.cwd(),
+        pnpmHomeDir: '',
+        rawConfig: {
+          registry: REGISTRY,
+        },
+        registries: { default: REGISTRY },
+        reporter,
+        storeDir: nonExistentStoreDir,
+        userConfig: {},
+        dlxCacheMaxAge: Infinity,
+        virtualStoreDirMaxLength: 120,
+      }, ['prune'])
+    ).resolves.toBeUndefined()
+
+    expect(reporter).toHaveBeenCalledWith(
+      expect.objectContaining({
+        level: 'info',
+        message: 'Removed 0 files',
+      })
+    )
+
+    expect(reporter).toHaveBeenCalledWith(
+      expect.objectContaining({
+        level: 'info',
+        message: 'Removed 0 packages',
+      })
+    )
+  })
+
+  test('prune will fail for other file-related errors (i.e.; not ENOENT)', async () => {
+    prepareEmpty()
+    const fileInPlaceOfStoreDir = path.resolve('store')
+    fs.writeFileSync(fileInPlaceOfStoreDir, '')
+    await expect(
+      store.handler({
+        cacheDir: path.resolve('cache'),
+        dir: process.cwd(),
+        pnpmHomeDir: '',
+        rawConfig: {
+          registry: REGISTRY,
+        },
+        registries: { default: REGISTRY },
+        reporter: jest.fn(),
+        storeDir: fileInPlaceOfStoreDir,
+        userConfig: {},
+        dlxCacheMaxAge: Infinity,
+        virtualStoreDirMaxLength: 120,
+      }, ['prune'])
+    ).rejects.toThrow(/^ENOTDIR/)
+  })
+})
+
 function createSampleDlxCacheLinkTarget (dirPath: string): void {
   fs.mkdirSync(path.join(dirPath, 'node_modules', '.pnpm'), { recursive: true })
   fs.mkdirSync(path.join(dirPath, 'node_modules', '.bin'), { recursive: true })