diff --git a/Source/Core/UICommon/AutoUpdate.cpp b/Source/Core/UICommon/AutoUpdate.cpp
index 0f1ea63d58..e1d6b7732c 100644
--- a/Source/Core/UICommon/AutoUpdate.cpp
+++ b/Source/Core/UICommon/AutoUpdate.cpp
@@ -84,6 +84,12 @@ void CleanupFromPreviousUpdate()
 {
   // Remove the relocated updater file.
   File::DeleteDirRecursively(UpdaterPath(true));
+
+  // Remove the old (non-embedded) updater app bundle.
+  // While the update process will delete the files within the old bundle after updating to a
+  // version with an embedded updater, it won't delete the folder structure of the bundle, so
+  // we should clean those leftovers up.
+  File::DeleteDirRecursively(File::GetExeDirectory() + DIR_SEP + "Dolphin Updater.app");
 }
 #endif