diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index b27c243fee..03f1fd4fad 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -517,6 +517,12 @@ static void EmuThread(std::unique_ptr<BootParameters> boot)
   if (!CBoot::BootUp(std::move(boot)))
     return;
 
+  // Initialise Wii filesystem contents.
+  // This is done here after Boot and not in HW to ensure that we operate
+  // with the correct title context since save copying requires title directories to exist.
+  Common::ScopeGuard wiifs_guard{Core::CleanUpWiiFileSystemContents};
+  Core::InitializeWiiFileSystemContents();
+
   // This adds the SyncGPU handler to CoreTiming, so now CoreTiming::Advance might block.
   Fifo::Prepare();
 
diff --git a/Source/Core/Core/HW/HW.cpp b/Source/Core/Core/HW/HW.cpp
index a60102bf7e..5cf808ee3f 100644
--- a/Source/Core/Core/HW/HW.cpp
+++ b/Source/Core/Core/HW/HW.cpp
@@ -54,13 +54,11 @@ void Init()
     Core::InitializeWiiRoot(Core::WantsDeterminism());
     IOS::Init();
     IOS::HLE::Init();  // Depends on Memory
-    Core::InitializeWiiFileSystemContents();
   }
 }
 
 void Shutdown()
 {
-  Core::CleanUpWiiFileSystemContents();
   // IOS should always be shut down regardless of bWii because it can be running in GC mode (MIOS).
   IOS::HLE::Shutdown();  // Depends on Memory
   IOS::Shutdown();