diff --git a/src/core/core.cpp b/src/core/core.cpp
index 054af8dc4a..046ee53346 100644
--- a/src/core/core.cpp
+++ b/src/core/core.cpp
@@ -312,6 +312,10 @@ struct System::Impl {
     }
 
     SystemResultStatus Load(System& system, Frontend::EmuWindow& emu_window, const std::string& filepath, Service::AM::FrontendAppletParameters& params) {
+        if (params.launch_type == Service::AM::LaunchType::FrontendInitiated) {
+            fs_controller.InitTempStorage();
+        }
+
         InitializeKernel(system);
 
         if (params.applet_type == Service::AM::AppletType::Application) {
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 306e8701c3..38d2f1735c 100644
--- a/src/core/hle/service/filesystem/filesystem.cpp
+++ b/src/core/hle/service/filesystem/filesystem.cpp
@@ -787,6 +787,13 @@ void FileSystemController::CreateFactories(FileSys::VfsFilesystem& vfs, bool ove
     }
 }
 
+void FileSystemController::InitTempStorage() {
+    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");
+    }
+}
+
 void FileSystemController::Reset() {
     std::scoped_lock lk{registration_lock};
     registrations.clear();
diff --git a/src/core/hle/service/filesystem/filesystem.h b/src/core/hle/service/filesystem/filesystem.h
index ef45aec627..a77358e2ef 100644
--- a/src/core/hle/service/filesystem/filesystem.h
+++ b/src/core/hle/service/filesystem/filesystem.h
@@ -127,6 +127,8 @@ public:
     // above is called.
     void CreateFactories(FileSys::VfsFilesystem& vfs, bool overwrite = true);
 
+    void InitTempStorage();
+
     void Reset();
 
 private: