diff --git a/.changeset/nested-filekvstore-list.md b/.changeset/nested-filekvstore-list.md
new file mode 100644
index 00000000..5883edb4
--- /dev/null
+++ b/.changeset/nested-filekvstore-list.md
@@ -0,0 +1,5 @@
+---
+"@tus/utils": patch
+---
+
+Fix `FileKvStore.list()` to include nested upload IDs. Expiration cleanup now removes existing nested uploads that meet the expiration rules, which were previously skipped.
diff --git a/packages/file-store/src/test/index.ts b/packages/file-store/src/test/index.ts
index f22e4654..953ad323 100644
--- a/packages/file-store/src/test/index.ts
+++ b/packages/file-store/src/test/index.ts
@@ -131,6 +131,30 @@ describe('FileStore', function () {
     })
   })
 
+  describe('deleteExpired', () => {
+    it('removes expired nested uploads and keeps unexpired uploads', async function () {
+      this.datastore.expirationPeriodInMilliseconds = 60_000
+      const expired = new Upload({
+        id: 'nested/path/expired',
+        size: 10,
+        offset: 0,
+        creation_date: new Date(Date.now() - 120_000).toISOString(),
+      })
+      const fresh = new Upload({id: 'nested/path/fresh', size: 10, offset: 0})
+      await this.datastore.create(expired)
+      await this.datastore.create(fresh)
+
+      assert.equal(await this.datastore.deleteExpired(), 1)
+      await assert.rejects(fsProm.stat(path.join(storePath, expired.id)), {
+        code: 'ENOENT',
+      })
+      await assert.rejects(fsProm.stat(path.join(storePath, `${expired.id}.json`)), {
+        code: 'ENOENT',
+      })
+      assert.equal((await this.datastore.getUpload(fresh.id)).id, fresh.id)
+    })
+  })
+
   describe('FileConfigstore', () => {
     it('should ignore random files in directory when calling list()', async () => {
       const store = new FileConfigstore(storePath)
diff --git a/packages/utils/src/kvstores/FileKvStore.ts b/packages/utils/src/kvstores/FileKvStore.ts
index 39ad0baa..20a92cd6 100644
--- a/packages/utils/src/kvstores/FileKvStore.ts
+++ b/packages/utils/src/kvstores/FileKvStore.ts
@@ -35,7 +35,20 @@ export class FileKvStore<T = Upload> implements KvStore<T> {
   }
 
   async list(): Promise<Array<string>> {
-    const files = new Set(await fs.readdir(this.directory))
+    const entries = await fs.readdir(this.directory, {
+      recursive: true,
+      withFileTypes: true,
+    })
+    const files = new Set(
+      entries
+        .filter((entry) => entry.isFile())
+        .map((entry) =>
+          path
+            .relative(this.directory, path.join(entry.parentPath, entry.name))
+            .split(path.sep)
+            .join('/')
+        )
+    )
     // To only return tus file IDs we check if the file has a corresponding JSON info file
     return [...files].filter((file) => files.has(`${file}.json`)).sort()
   }
diff --git a/packages/utils/src/test/FileKvStore.list.test.ts b/packages/utils/src/test/FileKvStore.list.test.ts
index ef126a72..5094f8e4 100644
--- a/packages/utils/src/test/FileKvStore.list.test.ts
+++ b/packages/utils/src/test/FileKvStore.list.test.ts
@@ -19,7 +19,13 @@ describe('FileKvStore', () => {
   })
 
   const touch = (...names: string[]) =>
-    Promise.all(names.map((name) => fs.writeFile(path.join(directory, name), '')))
+    Promise.all(
+      names.map(async (name) => {
+        const file = path.join(directory, name)
+        await fs.mkdir(path.dirname(file), {recursive: true})
+        await fs.writeFile(file, '')
+      })
+    )
 
   describe('list', () => {
     it('ignores unpaired files', async () => {
@@ -46,5 +52,38 @@ describe('FileKvStore', () => {
       await touch('b', 'b.json', 'c', 'c.json', 'a', 'a.json')
       assert.deepEqual(await store.list(), ['a', 'b', 'c'])
     })
+
+    it('lists nested ids with their full relative paths', async () => {
+      await touch(
+        'upload',
+        'upload.json',
+        'a/upload',
+        'a/upload.json',
+        'b/deep/upload',
+        'b/deep/upload.json'
+      )
+      assert.deepEqual(await store.list(), ['a/upload', 'b/deep/upload', 'upload'])
+    })
+
+    it('does not pair files across directories', async () => {
+      await touch('a/upload', 'b/upload.json')
+      assert.deepEqual(await store.list(), [])
+    })
+
+    it('ignores directories with a matching JSON file', async () => {
+      await fs.mkdir(path.join(directory, 'folder'))
+      await touch('folder.json')
+      assert.deepEqual(await store.list(), [])
+    })
+
+    it('does not follow directory symlinks', async () => {
+      await touch('real/upload', 'real/upload.json')
+      await fs.symlink(
+        path.join(directory, 'real'),
+        path.join(directory, 'link'),
+        'junction'
+      )
+      assert.deepEqual(await store.list(), ['real/upload'])
+    })
   })
 })