diff --git a/lib/private/IntegrityCheck/Checker.php b/lib/private/IntegrityCheck/Checker.php
index b17e4b1c0bfd3..32749a2c5f12a 100644
--- a/lib/private/IntegrityCheck/Checker.php
+++ b/lib/private/IntegrityCheck/Checker.php
@@ -356,8 +356,8 @@ private function verify(string $signaturePath, string $basePath, string $certifi
 
 		// Compare the list of files which are not identical
 		$currentInstanceHashes = $this->generateHashes($this->getFolderIterator($basePath), $basePath);
-		$differencesA = array_diff($expectedHashes, $currentInstanceHashes);
-		$differencesB = array_diff($currentInstanceHashes, $expectedHashes);
+		$differencesA = array_diff_assoc($expectedHashes, $currentInstanceHashes);
+		$differencesB = array_diff_assoc($currentInstanceHashes, $expectedHashes);
 		$differences = array_unique(array_merge($differencesA, $differencesB));
 		$differenceArray = [];
 		foreach ($differences as $filename => $hash) {