diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index 9b58f580e1..4dbe7a2f9d 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -45,6 +45,7 @@
 #include "Core/Movie.h"
 #include "Core/NetPlayProto.h"
 #include "Core/PowerPC/PowerPC.h"
+#include "Core/WiiRoot.h"
 
 #include "DiscIO/Enums.h"
 
@@ -439,7 +440,10 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
 
   // Ensure any new settings are written to the SYSCONF
   if (StartUp.bWii)
+  {
+    Core::BackupWiiSettings();
     ConfigLoaders::SaveToSYSCONF(Config::LayerType::Meta);
+  }
 
   const bool load_ipl = !StartUp.bWii && !StartUp.bHLE_BS2 &&
                         std::holds_alternative<BootParameters::Disc>(boot->parameters);
@@ -487,6 +491,7 @@ static void RestoreSYSCONF()
 
 void RestoreConfig()
 {
+  Core::RestoreWiiSettings(Core::RestoreReason::EmulationEnd);
   RestoreSYSCONF();
   Config::ClearCurrentRunLayer();
   Config::RemoveLayer(Config::LayerType::Movie);
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
index c5caf3b7b7..3b7a17ab97 100644
--- a/Source/Core/Core/WiiRoot.cpp
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -16,6 +16,8 @@
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
 #include "Common/NandPaths.h"
+#include "Common/StringUtil.h"
+#include "Core/CommonTitles.h"
 #include "Core/ConfigManager.h"
 #include "Core/HW/WiiSave.h"
 #include "Core/IOS/ES/ES.h"
@@ -32,6 +34,38 @@ namespace FS = IOS::HLE::FS;
 
 static std::string s_temp_wii_root;
 
+static bool CopyBackupFile(const std::string& path_from, const std::string& path_to)
+{
+  if (!File::Exists(path_from))
+    return false;
+
+  return File::Copy(path_from, path_to);
+}
+
+static void DeleteBackupFile(const std::string& file_name)
+{
+  File::Delete(File::GetUserPath(D_BACKUP_IDX) + DIR_SEP + file_name);
+}
+
+static void BackupFile(const std::string& path_in_nand)
+{
+  const std::string file_name = PathToFileName(path_in_nand);
+  const std::string original_path = File::GetUserPath(D_WIIROOT_IDX) + DIR_SEP + path_in_nand;
+  const std::string backup_path = File::GetUserPath(D_BACKUP_IDX) + DIR_SEP + file_name;
+
+  CopyBackupFile(original_path, backup_path);
+}
+
+static void RestoreFile(const std::string& path_in_nand)
+{
+  const std::string file_name = PathToFileName(path_in_nand);
+  const std::string original_path = File::GetUserPath(D_WIIROOT_IDX) + DIR_SEP + path_in_nand;
+  const std::string backup_path = File::GetUserPath(D_BACKUP_IDX) + DIR_SEP + file_name;
+
+  if (CopyBackupFile(backup_path, original_path))
+    DeleteBackupFile(file_name);
+}
+
 static void CopySave(FS::FileSystem* source, FS::FileSystem* dest, const u64 title_id)
 {
   dest->CreateFullPath(IOS::PID_KERNEL, IOS::PID_KERNEL, Common::GetTitleDataPath(title_id) + '/',
@@ -173,6 +207,29 @@ void ShutdownWiiRoot()
   }
 }
 
+void BackupWiiSettings()
+{
+  // Back up files which Dolphin can modify at boot, so that we can preserve the original contents.
+  // For SYSCONF, the backup is only needed in case Dolphin crashes or otherwise exists unexpectedly
+  // during emulation, since the config system will restore the SYSCONF settings at emulation end.
+  // For setting.txt, there is no other code that restores the original values for us.
+
+  BackupFile(Common::GetTitleDataPath(Titles::SYSTEM_MENU) + "/" WII_SETTING);
+  BackupFile("/shared2/sys/SYSCONF");
+}
+
+void RestoreWiiSettings(RestoreReason reason)
+{
+  RestoreFile(Common::GetTitleDataPath(Titles::SYSTEM_MENU) + "/" WII_SETTING);
+
+  // We must not restore the SYSCONF backup when ending emulation cleanly, since the user may have
+  // edited the SYSCONF file in the NAND using the emulated software (e.g. the Wii Menu settings).
+  if (reason == RestoreReason::CrashRecovery)
+    RestoreFile("/shared2/sys/SYSCONF");
+  else
+    DeleteBackupFile("SYSCONF");
+}
+
 /// Copy a directory from host_source_path (on the host FS) to nand_target_path on the NAND.
 ///
 /// Both paths should not have trailing slashes. To specify the NAND root, use "".
diff --git a/Source/Core/Core/WiiRoot.h b/Source/Core/Core/WiiRoot.h
index c62aaa103f..7b069d0c07 100644
--- a/Source/Core/Core/WiiRoot.h
+++ b/Source/Core/Core/WiiRoot.h
@@ -6,9 +6,18 @@
 
 namespace Core
 {
+enum class RestoreReason
+{
+  EmulationEnd,
+  CrashRecovery,
+};
+
 void InitializeWiiRoot(bool use_temporary);
 void ShutdownWiiRoot();
 
+void BackupWiiSettings();
+void RestoreWiiSettings(RestoreReason reason);
+
 // Initialize or clean up the filesystem contents.
 void InitializeWiiFileSystemContents();
 void CleanUpWiiFileSystemContents();
diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index 76ff64ac25..5af9192711 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -31,6 +31,7 @@
 #include "Core/HW/Wiimote.h"
 #include "Core/IOS/IOS.h"
 #include "Core/IOS/STM/STM.h"
+#include "Core/WiiRoot.h"
 
 #include "InputCommon/GCAdapter.h"
 
@@ -88,6 +89,8 @@ static void InitCustomPaths()
 
 void Init()
 {
+  Core::RestoreWiiSettings(Core::RestoreReason::CrashRecovery);
+
   Config::Init();
   Config::AddConfigChangedCallback(InitCustomPaths);
   Config::AddLayer(ConfigLoaders::GenerateBaseConfigLoader());