diff --git a/Source/Core/Core/BootManager.cpp b/Source/Core/Core/BootManager.cpp
index 40930117aa..ee60c6a946 100644
--- a/Source/Core/Core/BootManager.cpp
+++ b/Source/Core/Core/BootManager.cpp
@@ -91,7 +91,6 @@ private:
   int iSelectedLanguage = 0;
   PowerPC::CPUCore cpu_core = PowerPC::CPUCore::Interpreter;
   float m_EmulationSpeed = 0;
-  bool m_bt_passthrough_enabled = false;
   std::string m_strGPUDeterminismMode;
   std::array<WiimoteSource, MAX_BBMOTES> iWiimoteSource{};
   std::array<SerialInterface::SIDevices, SerialInterface::MAX_SI_CHANNELS> Pads{};
@@ -121,7 +120,6 @@ void ConfigCache::SaveConfig(const SConfig& config)
   cpu_core = config.cpu_core;
   m_EmulationSpeed = config.m_EmulationSpeed;
   m_strGPUDeterminismMode = config.m_strGPUDeterminismMode;
-  m_bt_passthrough_enabled = config.m_bt_passthrough_enabled;
 
   for (int i = 0; i != MAX_BBMOTES; ++i)
     iWiimoteSource[i] = WiimoteCommon::GetSource(i);
@@ -189,7 +187,6 @@ void ConfigCache::RestoreConfig(SConfig* config)
   }
 
   config->m_strGPUDeterminismMode = m_strGPUDeterminismMode;
-  config->m_bt_passthrough_enabled = m_bt_passthrough_enabled;
 }
 
 static ConfigCache config_cache;
@@ -357,7 +354,6 @@ bool BootCore(std::unique_ptr<BootParameters> boot, const WindowSystemInfo& wsi)
     StartUp.bMMU = netplay_settings.m_MMU;
     StartUp.bFastmem = netplay_settings.m_Fastmem;
     StartUp.bHLE_BS2 = netplay_settings.m_SkipIPL;
-    StartUp.m_bt_passthrough_enabled = false;
     if (netplay_settings.m_HostInputAuthority && !netplay_settings.m_IsHosting)
       config_cache.bSetEmulationSpeed = true;
   }
diff --git a/Source/Core/Core/Config/MainSettings.cpp b/Source/Core/Core/Config/MainSettings.cpp
index bf85875532..fdbe76d924 100644
--- a/Source/Core/Core/Config/MainSettings.cpp
+++ b/Source/Core/Core/Config/MainSettings.cpp
@@ -298,4 +298,13 @@ const Info<bool> MAIN_DEBUG_JIT_BRANCH_OFF{{System::Main, "Debug", "JitBranchOff
 const Info<bool> MAIN_DEBUG_JIT_REGISTER_CACHE_OFF{{System::Main, "Debug", "JitRegisterCacheOff"},
                                                    false};
 
+// Main.BluetoothPassthrough
+
+const Info<bool> MAIN_BLUETOOTH_PASSTHROUGH_ENABLED{
+    {System::Main, "BluetoothPassthrough", "Enabled"}, false};
+const Info<int> MAIN_BLUETOOTH_PASSTHROUGH_VID{{System::Main, "BluetoothPassthrough", "VID"}, -1};
+const Info<int> MAIN_BLUETOOTH_PASSTHROUGH_PID{{System::Main, "BluetoothPassthrough", "PID"}, -1};
+const Info<std::string> MAIN_BLUETOOTH_PASSTHROUGH_LINK_KEYS{
+    {System::Main, "BluetoothPassthrough", "LinkKeys"}, ""};
+
 }  // namespace Config
diff --git a/Source/Core/Core/Config/MainSettings.h b/Source/Core/Core/Config/MainSettings.h
index f3cd127231..87025dfc77 100644
--- a/Source/Core/Core/Config/MainSettings.h
+++ b/Source/Core/Core/Config/MainSettings.h
@@ -250,4 +250,11 @@ extern const Info<bool> MAIN_DEBUG_JIT_SYSTEM_REGISTERS_OFF;
 extern const Info<bool> MAIN_DEBUG_JIT_BRANCH_OFF;
 extern const Info<bool> MAIN_DEBUG_JIT_REGISTER_CACHE_OFF;
 
+// Main.BluetoothPassthrough
+
+extern const Info<bool> MAIN_BLUETOOTH_PASSTHROUGH_ENABLED;
+extern const Info<int> MAIN_BLUETOOTH_PASSTHROUGH_VID;
+extern const Info<int> MAIN_BLUETOOTH_PASSTHROUGH_PID;
+extern const Info<std::string> MAIN_BLUETOOTH_PASSTHROUGH_LINK_KEYS;
+
 }  // namespace Config
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
index 7acb9d625d..1ea385fddc 100644
--- a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
@@ -27,7 +27,8 @@ bool IsSettingSaveable(const Config::Location& config_location)
   {
     for (const std::string_view section :
          {"NetPlay", "General", "GBA", "Display", "Network", "Analytics", "AndroidOverlayButtons",
-          "DSP", "GameList", "FifoPlayer", "AutoUpdate", "Movie", "Input", "Debug"})
+          "DSP", "GameList", "FifoPlayer", "AutoUpdate", "Movie", "Input", "Debug",
+          "BluetoothPassthrough"})
     {
       if (config_location.section == section)
         return true;
diff --git a/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp
index c2eb753e28..128eba8ad7 100644
--- a/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/NetPlayConfigLoader.cpp
@@ -93,6 +93,8 @@ public:
 
     layer->Set(Config::SESSION_USE_FMA, m_settings.m_UseFMA);
 
+    layer->Set(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED, false);
+
     if (m_settings.m_StrictSettingsSync)
     {
       layer->Set(Config::GFX_HACK_VERTEX_ROUDING, m_settings.m_VertexRounding);
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index 7ad9458b81..2d44656ae6 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -91,7 +91,6 @@ void SConfig::SaveSettings()
   SaveGeneralSettings(ini);
   SaveInterfaceSettings(ini);
   SaveCoreSettings(ini);
-  SaveBluetoothPassthroughSettings(ini);
   SaveUSBPassthroughSettings(ini);
 
   ini.Save(File::GetUserPath(F_DOLPHINCONFIG_IDX));
@@ -196,16 +195,6 @@ void SConfig::SaveCoreSettings(IniFile& ini)
   core->Set("CustomRTCValue", m_customRTCValue);
 }
 
-void SConfig::SaveBluetoothPassthroughSettings(IniFile& ini)
-{
-  IniFile::Section* section = ini.GetOrCreateSection("BluetoothPassthrough");
-
-  section->Set("Enabled", m_bt_passthrough_enabled);
-  section->Set("VID", m_bt_passthrough_vid);
-  section->Set("PID", m_bt_passthrough_pid);
-  section->Set("LinkKeys", m_bt_passthrough_link_keys);
-}
-
 void SConfig::SaveUSBPassthroughSettings(IniFile& ini)
 {
   IniFile::Section* section = ini.GetOrCreateSection("USBPassthrough");
@@ -231,7 +220,6 @@ void SConfig::LoadSettings()
   LoadGeneralSettings(ini);
   LoadInterfaceSettings(ini);
   LoadCoreSettings(ini);
-  LoadBluetoothPassthroughSettings(ini);
   LoadUSBPassthroughSettings(ini);
 }
 
@@ -341,16 +329,6 @@ void SConfig::LoadCoreSettings(IniFile& ini)
   core->Get("CustomRTCValue", &m_customRTCValue, 946684800);
 }
 
-void SConfig::LoadBluetoothPassthroughSettings(IniFile& ini)
-{
-  IniFile::Section* section = ini.GetOrCreateSection("BluetoothPassthrough");
-
-  section->Get("Enabled", &m_bt_passthrough_enabled, false);
-  section->Get("VID", &m_bt_passthrough_vid, -1);
-  section->Get("PID", &m_bt_passthrough_pid, -1);
-  section->Get("LinkKeys", &m_bt_passthrough_link_keys, "");
-}
-
 void SConfig::LoadUSBPassthroughSettings(IniFile& ini)
 {
   IniFile::Section* section = ini.GetOrCreateSection("USBPassthrough");
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index 3219b01d7c..e206dba83e 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -128,12 +128,6 @@ struct SConfig
   bool bLockCursor = false;
   std::string theme_name;
 
-  // Bluetooth passthrough mode settings
-  bool m_bt_passthrough_enabled = false;
-  int m_bt_passthrough_pid = -1;
-  int m_bt_passthrough_vid = -1;
-  std::string m_bt_passthrough_link_keys;
-
   // USB passthrough settings
   std::set<std::pair<u16, u16>> m_usb_passthrough_devices;
   bool IsUSBDeviceWhitelisted(std::pair<u16, u16> vid_pid) const;
@@ -243,13 +237,11 @@ private:
   void SaveGeneralSettings(IniFile& ini);
   void SaveInterfaceSettings(IniFile& ini);
   void SaveCoreSettings(IniFile& ini);
-  void SaveBluetoothPassthroughSettings(IniFile& ini);
   void SaveUSBPassthroughSettings(IniFile& ini);
 
   void LoadGeneralSettings(IniFile& ini);
   void LoadInterfaceSettings(IniFile& ini);
   void LoadCoreSettings(IniFile& ini);
-  void LoadBluetoothPassthroughSettings(IniFile& ini);
   void LoadUSBPassthroughSettings(IniFile& ini);
 
   void SetRunningGameMetadata(const std::string& game_id, const std::string& gametdb_id,
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 6419d13e61..99cd305082 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -486,7 +486,7 @@ static void EmuThread(std::unique_ptr<BootParameters> boot, WindowSystemInfo wsi
 
   // Load and Init Wiimotes - only if we are booting in Wii mode
   bool init_wiimotes = false;
-  if (core_parameter.bWii && !SConfig::GetInstance().m_bt_passthrough_enabled)
+  if (core_parameter.bWii && !Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
   {
     if (init_controllers)
     {
diff --git a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
index b3c5b1f203..06ae8e790a 100644
--- a/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
+++ b/Source/Core/Core/HW/WiimoteReal/WiimoteReal.cpp
@@ -681,7 +681,7 @@ void WiimoteScanner::ThreadFunc()
     {
       // We don't want any remotes in passthrough mode or running in GC mode.
       const bool core_running = Core::GetState() != Core::State::Uninitialized;
-      if (SConfig::GetInstance().m_bt_passthrough_enabled ||
+      if (Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED) ||
           (core_running && !SConfig::GetInstance().bWii))
         continue;
 
diff --git a/Source/Core/Core/IOS/IOS.cpp b/Source/Core/Core/IOS/IOS.cpp
index 53c99ddaf9..6fedd7ebc4 100644
--- a/Source/Core/Core/IOS/IOS.cpp
+++ b/Source/Core/Core/IOS/IOS.cpp
@@ -515,7 +515,7 @@ void Kernel::AddStaticDevices()
 
   // OH1 (Bluetooth)
   AddDevice(std::make_unique<DeviceStub>(*this, "/dev/usb/oh1"));
-  if (!SConfig::GetInstance().m_bt_passthrough_enabled)
+  if (!Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
     AddDevice(std::make_unique<BluetoothEmuDevice>(*this, "/dev/usb/oh1/57e/305"));
   else
     AddDevice(std::make_unique<BluetoothRealDevice>(*this, "/dev/usb/oh1/57e/305"));
diff --git a/Source/Core/Core/IOS/USB/Bluetooth/BTReal.cpp b/Source/Core/Core/IOS/USB/Bluetooth/BTReal.cpp
index 10aa72c3b5..3144580212 100644
--- a/Source/Core/Core/IOS/USB/Bluetooth/BTReal.cpp
+++ b/Source/Core/Core/IOS/USB/Bluetooth/BTReal.cpp
@@ -24,7 +24,7 @@
 #include "Common/Network.h"
 #include "Common/StringUtil.h"
 #include "Common/Swap.h"
-#include "Core/ConfigManager.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/Core.h"
 #include "Core/HW/Memmap.h"
 #include "Core/IOS/Device.h"
@@ -38,8 +38,8 @@ constexpr u8 REQUEST_TYPE = static_cast<u8>(LIBUSB_ENDPOINT_OUT) |
 
 static bool IsWantedDevice(const libusb_device_descriptor& descriptor)
 {
-  const int vid = SConfig::GetInstance().m_bt_passthrough_vid;
-  const int pid = SConfig::GetInstance().m_bt_passthrough_pid;
+  const int vid = Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_VID);
+  const int pid = Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_PID);
   if (vid == -1 || pid == -1)
     return true;
   return descriptor.idVendor == vid && descriptor.idProduct == pid;
@@ -49,9 +49,11 @@ static bool IsBluetoothDevice(const libusb_interface_descriptor& descriptor)
 {
   constexpr u8 SUBCLASS = 0x01;
   constexpr u8 PROTOCOL_BLUETOOTH = 0x01;
-  if (SConfig::GetInstance().m_bt_passthrough_vid != -1 &&
-      SConfig::GetInstance().m_bt_passthrough_pid != -1)
+  if (Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_VID) != -1 &&
+      Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_PID) != -1)
+  {
     return true;
+  }
   return descriptor.bInterfaceClass == LIBUSB_CLASS_WIRELESS &&
          descriptor.bInterfaceSubClass == SUBCLASS &&
          descriptor.bInterfaceProtocol == PROTOCOL_BLUETOOTH;
@@ -499,7 +501,7 @@ void BluetoothRealDevice::FakeSyncButtonHeldEvent(USB::V0IntrMessage& ctrl)
 
 void BluetoothRealDevice::LoadLinkKeys()
 {
-  const std::string& entries = SConfig::GetInstance().m_bt_passthrough_link_keys;
+  std::string entries = Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_LINK_KEYS);
   if (entries.empty())
     return;
   for (const auto& pair : SplitString(entries, ','))
@@ -556,7 +558,7 @@ void BluetoothRealDevice::SaveLinkKeys()
   std::string config_string = oss.str();
   if (!config_string.empty())
     config_string.pop_back();
-  SConfig::GetInstance().m_bt_passthrough_link_keys = config_string;
+  Config::SetBase(Config::MAIN_BLUETOOTH_PASSTHROUGH_LINK_KEYS, config_string);
 }
 
 bool BluetoothRealDevice::OpenDevice(libusb_device* device)
diff --git a/Source/Core/Core/WiiUtils.cpp b/Source/Core/Core/WiiUtils.cpp
index 14dbaf5bed..8bb48ad6b1 100644
--- a/Source/Core/Core/WiiUtils.cpp
+++ b/Source/Core/Core/WiiUtils.cpp
@@ -29,7 +29,7 @@
 #include "Common/StringUtil.h"
 #include "Common/Swap.h"
 #include "Core/CommonTitles.h"
-#include "Core/ConfigManager.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/IOS/Device.h"
 #include "Core/IOS/ES/ES.h"
 #include "Core/IOS/ES/Formats.h"
@@ -967,14 +967,14 @@ static std::shared_ptr<IOS::HLE::Device> GetBluetoothDevice()
 
 std::shared_ptr<IOS::HLE::BluetoothEmuDevice> GetBluetoothEmuDevice()
 {
-  if (SConfig::GetInstance().m_bt_passthrough_enabled)
+  if (Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
     return nullptr;
   return std::static_pointer_cast<IOS::HLE::BluetoothEmuDevice>(GetBluetoothDevice());
 }
 
 std::shared_ptr<IOS::HLE::BluetoothRealDevice> GetBluetoothRealDevice()
 {
-  if (!SConfig::GetInstance().m_bt_passthrough_enabled)
+  if (!Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
     return nullptr;
   return std::static_pointer_cast<IOS::HLE::BluetoothRealDevice>(GetBluetoothDevice());
 }
diff --git a/Source/Core/DolphinQt/Config/WiimoteControllersWidget.cpp b/Source/Core/DolphinQt/Config/WiimoteControllersWidget.cpp
index fbfb853d7f..70a65f5752 100644
--- a/Source/Core/DolphinQt/Config/WiimoteControllersWidget.cpp
+++ b/Source/Core/DolphinQt/Config/WiimoteControllersWidget.cpp
@@ -17,6 +17,7 @@
 #include <map>
 #include <optional>
 
+#include "Core/Config/MainSettings.h"
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/HW/Wiimote.h"
@@ -308,7 +309,7 @@ void WiimoteControllersWidget::LoadSettings()
   m_wiimote_ciface->setChecked(SConfig::GetInstance().connect_wiimotes_for_ciface);
   m_wiimote_continuous_scanning->setChecked(SConfig::GetInstance().m_WiimoteContinuousScanning);
 
-  if (SConfig::GetInstance().m_bt_passthrough_enabled)
+  if (Config::Get(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED))
     m_wiimote_passthrough->setChecked(true);
   else
     m_wiimote_emu->setChecked(true);
@@ -321,7 +322,8 @@ void WiimoteControllersWidget::SaveSettings()
   SConfig::GetInstance().m_WiimoteEnableSpeaker = m_wiimote_speaker_data->isChecked();
   SConfig::GetInstance().connect_wiimotes_for_ciface = m_wiimote_ciface->isChecked();
   SConfig::GetInstance().m_WiimoteContinuousScanning = m_wiimote_continuous_scanning->isChecked();
-  SConfig::GetInstance().m_bt_passthrough_enabled = m_wiimote_passthrough->isChecked();
+  Config::SetBaseOrCurrent(Config::MAIN_BLUETOOTH_PASSTHROUGH_ENABLED,
+                           m_wiimote_passthrough->isChecked());
 
   WiimoteCommon::SetSource(WIIMOTE_BALANCE_BOARD, m_wiimote_real_balance_board->isChecked() ?
                                                       WiimoteSource::Real :