diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index a339ee80dd..617d51c24d 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -433,11 +433,23 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
   if (StartUp.bWii && DiscIO::IsNTSC(StartUp.m_region) && Config::Get(Config::SYSCONF_PAL60))
     Config::SetCurrent(Config::SYSCONF_PAL60, false);
 
-  // Ensure any new settings are written to the SYSCONF
   if (StartUp.bWii)
   {
-    Core::BackupWiiSettings();
-    ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta);
+    const bool want_determinism = Movie::IsMovieActive() || NetPlay::IsNetPlayRunning();
+    Core::InitializeWiiRoot(want_determinism);
+
+    // Ensure any new settings are written to the SYSCONF
+    if (!want_determinism)
+    {
+      Core::BackupWiiSettings();
+      ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta);
+    }
+    else
+    {
+      ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta, [](const Config::Location& location) {
+        return Config::GetActiveLayerForConfig(location) >= Config::LayerType::Movie;
+      });
+    }
   }
 
   const bool load_ipl = !StartUp.bWii && !StartUp.bHLE_BS2 &&
@@ -486,8 +498,14 @@ static void RestoreSYSCONF()
 
 void RestoreConfig()
 {
-  Core::RestoreWiiSettings(Core::RestoreReason::EmulationEnd);
-  RestoreSYSCONF();
+  Core::ShutdownWiiRoot();
+
+  if (!Core::WiiRootIsTemporary())
+  {
+    Core::RestoreWiiSettings(Core::RestoreReason::EmulationEnd);
+    RestoreSYSCONF();
+  }
+
   Config::ClearCurrentRunLayer();
   Config::RemoveLayer(Config::LayerType::Movie);
   Config::RemoveLayer(Config::LayerType::Netplay);
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index 65b46ec4bd..d3e340c68d 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -6,6 +6,7 @@
 
 #include <algorithm>
 #include <cstring>
+#include <functional>
 #include <list>
 #include <map>
 #include <memory>
@@ -29,7 +30,7 @@
 
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::LayerType layer)
+void SaveToSYSCONF(Config::LayerType layer, std::function<bool(const Config::Location&)> predicate)
 {
   if (Core::IsRunning())
     return;
@@ -40,7 +41,10 @@ void SaveToSYSCONF(Config::LayerType layer)
   for (const Config::SYSCONFSetting& setting : Config::SYSCONF_SETTINGS)
   {
     std::visit(
-        [layer, &setting, &sysconf](auto* info) {
+        [&](auto* info) {
+          if (predicate && !predicate(info->GetLocation()))
+            return;
+
           const std::string key = info->GetLocation().section + "." + info->GetLocation().key;
 
           if (setting.type == SysConf::Entry::Type::Long)
diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
index 2082e405b3..1fc28674f5 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.h
@@ -4,16 +4,19 @@
 
 #pragma once
 
+#include <functional>
 #include <memory>
 
 namespace Config
 {
 class ConfigLayerLoader;
 enum class LayerType;
+struct Location;
 }  // namespace Config
 
 namespace ConfigLoaders
 {
-void SaveToSYSCONF(Config::LayerType layer);
+void SaveToSYSCONF(Config::LayerType layer,
+                   std::function<bool(const Config::Location&)> predicate = {});
 std::unique_ptr<Config::ConfigLayerLoader> GenerateBaseConfigLoader();
 }  // namespace ConfigLoaders
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 99e7624b55..2fe18a7e67 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -590,7 +590,7 @@ static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi
     return;
 
   // Initialise Wii filesystem contents.
-  // This is done here after Boot and not in HW to ensure that we operate
+  // This is done here after Boot and not in BootManager to ensure that we operate
   // with the correct title context since save copying requires title directories to exist.
   Common::ScopeGuard wiifs_guard{&Core::CleanUpWiiFileSystemContents};
   if (SConfig::GetInstance().bWii)
diff --git a/Source/Core/Core/HW/HW.cpp b/Source/Core/Core/HW/HW.cpp
index 654164d960..6e2cf7d17b 100644
--- a/Source/Core/Core/HW/HW.cpp
+++ b/Source/Core/Core/HW/HW.cpp
@@ -25,7 +25,6 @@
 #include "Core/HW/WII_IPC.h"
 #include "Core/IOS/IOS.h"
 #include "Core/State.h"
-#include "Core/WiiRoot.h"
 
 namespace HW
 {
@@ -52,8 +51,6 @@ void Init()
 
   if (SConfig::GetInstance().bWii)
   {
-    // The NAND should only be initialised once per emulation session.
-    Core::InitializeWiiRoot(Core::WantsDeterminism());
     IOS::Init();
     IOS::HLE::Init();  // Depends on Memory
   }
@@ -64,7 +61,6 @@ void Shutdown()
   // 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();
-  Core::ShutdownWiiRoot();
 
   SystemTimers::Shutdown();
   CPU::Shutdown();
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index b042edc039..9503b70b9e 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -202,13 +202,18 @@ void InitializeWiiRoot(bool use_temporary)
 
 void ShutdownWiiRoot()
 {
-  if (!s_temp_wii_root.empty())
+  if (WiiRootIsTemporary())
   {
     File::DeleteDirRecursively(s_temp_wii_root);
     s_temp_wii_root.clear();
   }
 }
 
+bool WiiRootIsTemporary()
+{
+  return !s_temp_wii_root.empty();
+}
+
 void BackupWiiSettings()
 {
   // Back up files which Dolphin can modify at boot, so that we can preserve the original contents.
@@ -282,7 +287,7 @@ void InitializeWiiFileSystemContents()
   if (!CopySysmenuFilesToFS(fs.get(), File::GetSysDirectory() + WII_USER_DIR, ""))
     WARN_LOG_FMT(CORE, "Failed to copy initial System Menu files to the NAND");
 
-  if (s_temp_wii_root.empty())
+  if (!WiiRootIsTemporary())
     return;
 
   // Generate a SYSCONF with default settings for the temporary Wii NAND.
@@ -294,7 +299,7 @@ void InitializeWiiFileSystemContents()
 
 void CleanUpWiiFileSystemContents()
 {
-  if (s_temp_wii_root.empty() || !SConfig::GetInstance().bEnableMemcardSdWriting ||
+  if (!WiiRootIsTemporary() || !SConfig::GetInstance().bEnableMemcardSdWriting ||
       NetPlay::GetWiiSyncFS())
   {
     return;
diff --git a/Source/Core/Core/WiiRoot.h b/Source/Core/Core/WiiRoot.h
index 7b069d0c07..ad4ac609b9 100644
--- a/Source/Core/Core/WiiRoot.h
+++ b/Source/Core/Core/WiiRoot.h
@@ -15,6 +15,8 @@ enum class RestoreReason
 void InitializeWiiRoot(bool use_temporary);
 void ShutdownWiiRoot();
 
+bool WiiRootIsTemporary();
+
 void BackupWiiSettings();
 void RestoreWiiSettings(RestoreReason reason);