diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 683fa9cf6f..11494c4cb5 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -383,7 +383,6 @@ static void CpuThread(Core::System& system, const std::optional<std::string>& sa
   if (exception_handler)
   {
     EMM::InstallExceptionHandler();
-    system.GetMemory().InitDirtyPages();
   }
 #ifdef USE_MEMORYWATCHER
   s_memory_watcher = std::make_unique<MemoryWatcher>();
@@ -689,6 +688,9 @@ static void EmuThread(Core::System& system, std::unique_ptr<BootParameters> boot
     cpuThreadFunc(system, savestate_path, delete_savestate);
   }
 
+  if (cpuThreadFunc == CpuThread)
+    system.GetMemory().InitDirtyPages();
+
   INFO_LOG_FMT(CONSOLE, "{}", StopMessage(true, "Stopping GDB ..."));
   GDBStub::Deinit();
   INFO_LOG_FMT(CONSOLE, "{}", StopMessage(true, "GDB stopped."));
diff --git a/Source/Core/Core/HW/Memmap.cpp b/Source/Core/Core/HW/Memmap.cpp
index a1ac3d4b28..1e87f414b0 100644
--- a/Source/Core/Core/HW/Memmap.cpp
+++ b/Source/Core/Core/HW/Memmap.cpp
@@ -90,7 +90,8 @@ void MemoryManager::WriteProtectPhysicalMemoryRegions()
                     reinterpret_cast<u64>(*region.out_pointer));
     }
     const size_t page_size = Common::PageSize();
-    for (size_t i = reinterpret_cast<intptr_t>(*region.out_pointer); i < region.size; i += page_size)
+    const intptr_t out_pointer = reinterpret_cast<intptr_t>(*region.out_pointer);
+    for (size_t i = out_pointer; i < region.size; i += page_size)
     {
       m_dirty_pages[i] = false;
     }
@@ -154,7 +155,8 @@ void MemoryManager::Init()
   m_physical_regions[1] = PhysicalMemoryRegion{
       &m_l1_cache, 0xE0000000, GetL1CacheSize(), PhysicalMemoryRegion::ALWAYS, 0, false, false};
   m_physical_regions[2] = PhysicalMemoryRegion{
-      &m_fake_vmem, 0x7E000000, GetFakeVMemSize(), PhysicalMemoryRegion::FAKE_VMEM, 0, false, false};
+      &m_fake_vmem, 0x7E000000, GetFakeVMemSize(), PhysicalMemoryRegion::FAKE_VMEM, 0,
+      false,        false};
   m_physical_regions[3] = PhysicalMemoryRegion{
       &m_exram, 0x10000000, GetExRamSize(), PhysicalMemoryRegion::WII_ONLY, 0, false, true};
 
@@ -408,23 +410,11 @@ void MemoryManager::DoState(PointerWrap& p, bool delta)
         p.DoArray(m_ram + i, page_size);
       }
     }
-    for (size_t i = 0; i < current_l1_cache_size; i += page_size)
-    {
-      if (IsPageDirty(reinterpret_cast<uintptr_t>(&m_l1_cache[i])))
-      {
-        p.DoArray(m_l1_cache + i, page_size);
-      }
-    }
+    p.DoArray(m_l1_cache, current_l1_cache_size);
     p.DoMarker("Memory RAM");
     if (current_have_fake_vmem)
     {
-      for (size_t i = 0; i < current_fake_vmem_size; i += page_size)
-      {
-        if (IsPageDirty(reinterpret_cast<uintptr_t>(&m_fake_vmem[i])))
-        {
-          p.DoArray(m_fake_vmem + i, page_size);
-        }
-      }
+      p.DoArray(m_fake_vmem, current_fake_vmem_size);
     }
     p.DoMarker("Memory FakeVMEM");
     if (current_have_exram)
@@ -456,13 +446,13 @@ void MemoryManager::DoState(PointerWrap& p, bool delta)
 void MemoryManager::Shutdown()
 {
   ShutdownFastmemArena();
+  m_dirty_pages.clear();
 
   m_is_initialized = false;
   for (const PhysicalMemoryRegion& region : m_physical_regions)
   {
     if (!region.active)
       continue;
-
     m_arena.ReleaseView(*region.out_pointer, region.size);
     *region.out_pointer = nullptr;
   }
diff --git a/Source/Core/Core/HW/Memmap.h b/Source/Core/Core/HW/Memmap.h
index 834525b9f8..a9b6e52531 100644
--- a/Source/Core/Core/HW/Memmap.h
+++ b/Source/Core/Core/HW/Memmap.h
@@ -137,7 +137,6 @@ public:
   bool IsPageDirty(uintptr_t address);
   void SetPageDirtyBit(uintptr_t address, size_t size, bool dirty);
   void ResetDirtyPages();
-  bool VirtualProtectMemory(u8* data, size_t size, u64 flag);
   bool HandleFault(uintptr_t fault_address);
 
   std::map<u64, u8>& GetDirtyPages() { return m_dirty_pages; }