diff --git a/src/core/file_sys/savedata_factory.cpp b/src/core/file_sys/savedata_factory.cpp
index 0ba839ec14..c756734a43 100644
--- a/src/core/file_sys/savedata_factory.cpp
+++ b/src/core/file_sys/savedata_factory.cpp
@@ -57,11 +57,7 @@ std::string GetFutureSaveDataPath(SaveDataSpaceId space_id, SaveDataType type, u
 
 SaveDataFactory::SaveDataFactory(Core::System& system_, ProgramId program_id_,
                                  VirtualDir save_directory_)
-    : system{system_}, program_id{program_id_}, dir{std::move(save_directory_)} {
-    // Delete all temporary storages
-    // On hardware, it is expected that temporary storage be empty at first use.
-    dir->DeleteSubdirectoryRecursive("temp");
-}
+    : system{system_}, program_id{program_id_}, dir{std::move(save_directory_)} {}
 
 SaveDataFactory::~SaveDataFactory() = default;
 
diff --git a/src/core/hle/service/filesystem/filesystem.cpp b/src/core/hle/service/filesystem/filesystem.cpp
index 20e050c8a8..5e3822d29f 100644
--- a/src/core/hle/service/filesystem/filesystem.cpp
+++ b/src/core/hle/service/filesystem/filesystem.cpp
@@ -336,6 +336,10 @@ Result FileSystemController::RegisterProcess(
     ProcessId process_id, ProgramId program_id,
     std::shared_ptr<FileSys::RomFSFactory>&& romfs_factory) {
     std::scoped_lock lk{registration_lock};
+    if (registrations.empty()) {
+        const auto save_directory = system.GetFilesystem()->OpenDirectory(Common::FS::GetEdenPathString(Common::FS::EdenPath::SaveDir), FileSys::OpenMode::ReadWrite);
+        if (save_directory != nullptr) save_directory->DeleteSubdirectoryRecursive("temp");
+    }
 
     registrations.emplace(process_id, Registration{
                                           .program_id = program_id,