diff --git a/apps/files/appinfo/info.xml b/apps/files/appinfo/info.xml
index c5b1e85f9b..5f1ef494b7 100644
--- a/apps/files/appinfo/info.xml
+++ b/apps/files/appinfo/info.xml
@@ -34,6 +34,7 @@
 		<command>OCA\Files\Command\DeleteOrphanedFiles</command>
 		<command>OCA\Files\Command\TransferOwnership</command>
 		<command>OCA\Files\Command\ScanAppData</command>
+		<command>OCA\Files\Command\RepairTree</command>
 	</commands>
 
 	<activity>
diff --git a/apps/files/composer/composer/autoload_classmap.php b/apps/files/composer/composer/autoload_classmap.php
index a4a72d59c1..73104f155f 100644
--- a/apps/files/composer/composer/autoload_classmap.php
+++ b/apps/files/composer/composer/autoload_classmap.php
@@ -28,6 +28,7 @@ return array(
     'OCA\\Files\\Collaboration\\Resources\\Listener' => $baseDir . '/../lib/Collaboration/Resources/Listener.php',
     'OCA\\Files\\Collaboration\\Resources\\ResourceProvider' => $baseDir . '/../lib/Collaboration/Resources/ResourceProvider.php',
     'OCA\\Files\\Command\\DeleteOrphanedFiles' => $baseDir . '/../lib/Command/DeleteOrphanedFiles.php',
+    'OCA\\Files\\Command\\RepairTree' => $baseDir . '/../lib/Command/RepairTree.php',
     'OCA\\Files\\Command\\Scan' => $baseDir . '/../lib/Command/Scan.php',
     'OCA\\Files\\Command\\ScanAppData' => $baseDir . '/../lib/Command/ScanAppData.php',
     'OCA\\Files\\Command\\TransferOwnership' => $baseDir . '/../lib/Command/TransferOwnership.php',
diff --git a/apps/files/composer/composer/autoload_static.php b/apps/files/composer/composer/autoload_static.php
index 91e29fac48..cc360c9891 100644
--- a/apps/files/composer/composer/autoload_static.php
+++ b/apps/files/composer/composer/autoload_static.php
@@ -43,6 +43,7 @@ class ComposerStaticInitFiles
         'OCA\\Files\\Collaboration\\Resources\\Listener' => __DIR__ . '/..' . '/../lib/Collaboration/Resources/Listener.php',
         'OCA\\Files\\Collaboration\\Resources\\ResourceProvider' => __DIR__ . '/..' . '/../lib/Collaboration/Resources/ResourceProvider.php',
         'OCA\\Files\\Command\\DeleteOrphanedFiles' => __DIR__ . '/..' . '/../lib/Command/DeleteOrphanedFiles.php',
+        'OCA\\Files\\Command\\RepairTree' => __DIR__ . '/..' . '/../lib/Command/RepairTree.php',
         'OCA\\Files\\Command\\Scan' => __DIR__ . '/..' . '/../lib/Command/Scan.php',
         'OCA\\Files\\Command\\ScanAppData' => __DIR__ . '/..' . '/../lib/Command/ScanAppData.php',
         'OCA\\Files\\Command\\TransferOwnership' => __DIR__ . '/..' . '/../lib/Command/TransferOwnership.php',
diff --git a/apps/files/lib/Command/RepairTree.php b/apps/files/lib/Command/RepairTree.php
new file mode 100644
index 0000000000..77b97d7ca0
--- /dev/null
+++ b/apps/files/lib/Command/RepairTree.php
@@ -0,0 +1,107 @@
+<?php
+
+declare(strict_types=1);
+/**
+ * @copyright Copyright (c) 2021 Robin Appelman <robin@icewind.nl>
+ *
+ * @license GNU AGPL version 3 or any later version
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+namespace OCA\Files\Command;
+
+use OCP\IDBConnection;
+use Symfony\Component\Console\Command\Command;
+use Symfony\Component\Console\Input\InputInterface;
+use Symfony\Component\Console\Output\OutputInterface;
+
+class RepairTree extends Command {
+	public const CHUNK_SIZE = 200;
+
+	/**
+	 * @var IDBConnection
+	 */
+	protected $connection;
+
+	public function __construct(IDBConnection $connection) {
+		$this->connection = $connection;
+		parent::__construct();
+	}
+
+	protected function configure() {
+		$this
+			->setName('files:repair-tree')
+			->setDescription('Try and repair malformed filesystem tree structures')
+			->addOption('dry-run');
+	}
+
+	public function execute(InputInterface $input, OutputInterface $output): int {
+		$rows = $this->findBrokenTreeBits();
+		$fix = !$input->getOption('dry-run');
+
+		$output->writeln("Found " . count($rows) . " file entries with an invalid path");
+
+		if ($fix) {
+			$this->connection->beginTransaction();
+		}
+
+		$query = $this->connection->getQueryBuilder();
+		$query->update('filecache')
+			->set('path', $query->createParameter('path'))
+			->set('path_hash', $query->func()->md5($query->createParameter('path')))
+			->where($query->expr()->eq('fileid', $query->createParameter('fileid')));
+
+		foreach ($rows as $row) {
+			$output->writeln("Path of file ${row['fileid']} is ${row['path']} but should be ${row['parent_path']}/${row['name']} based on it's parent", OutputInterface::VERBOSITY_VERBOSE);
+
+			if ($fix) {
+				$query->setParameters([
+					'fileid' => $row['fileid'],
+					'path' => $row['parent_path'] . '/' . $row['name'],
+				]);
+				$query->execute();
+			}
+		}
+
+		if ($fix) {
+			$this->connection->commit();
+		}
+
+		return 0;
+	}
+
+	private function findBrokenTreeBits(): array {
+		$query = $this->connection->getQueryBuilder();
+
+		$query->select('f.fileid', 'f.path', 'f.parent', 'f.name')
+			->selectAlias('p.path', 'parent_path')
+			->from('filecache', 'f')
+			->innerJoin('f', 'filecache', 'p', $query->expr()->eq('f.parent', 'p.fileid'))
+			->where($query->expr()->orX(
+				$query->expr()->andX(
+					$query->expr()->neq('p.path_hash', $query->createNamedParameter(md5(''))),
+					$query->expr()->neq('f.path', $query->func()->concat('p.path', $query->func()->concat($query->createNamedParameter('/'), 'f.name')))
+				),
+				$query->expr()->andX(
+					$query->expr()->eq('p.path_hash', $query->createNamedParameter(md5(''))),
+					$query->expr()->neq('f.path', 'f.name')
+				),
+				$query->expr()->neq('f.storage', 'p.storage')
+			));
+
+		return $query->execute()->fetchAll();
+	}
+}