diff --git a/Source/Core/Core/Config/MainSettings.cpp b/Source/Core/Core/Config/MainSettings.cpp
index 3521b59a8a..291566bd9d 100644
--- a/Source/Core/Core/Config/MainSettings.cpp
+++ b/Source/Core/Core/Config/MainSettings.cpp
@@ -270,4 +270,8 @@ const Info<bool> MAIN_MOVIE_SHOW_INPUT_DISPLAY{{System::Main, "Movie", "ShowInpu
 const Info<bool> MAIN_MOVIE_SHOW_RTC{{System::Main, "Movie", "ShowRTC"}, false};
 const Info<bool> MAIN_MOVIE_SHOW_RERECORD{{System::Main, "Movie", "ShowRerecord"}, false};
 
+// Main.Input
+
+const Info<bool> MAIN_INPUT_BACKGROUND_INPUT{{System::Main, "Input", "BackgroundInput"}, false};
+
 }  // namespace Config
diff --git a/Source/Core/Core/Config/MainSettings.h b/Source/Core/Core/Config/MainSettings.h
index a0795729ff..8bf74f7e5b 100644
--- a/Source/Core/Core/Config/MainSettings.h
+++ b/Source/Core/Core/Config/MainSettings.h
@@ -230,4 +230,8 @@ extern const Info<bool> MAIN_MOVIE_SHOW_INPUT_DISPLAY;
 extern const Info<bool> MAIN_MOVIE_SHOW_RTC;
 extern const Info<bool> MAIN_MOVIE_SHOW_RERECORD;
 
+// Main.Input
+
+extern const Info<bool> MAIN_INPUT_BACKGROUND_INPUT;
+
 }  // namespace Config
diff --git a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
index 4abd8ee147..4a197eea30 100644
--- a/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
+++ b/Source/Core/Core/ConfigLoaders/IsSettingSaveable.cpp
@@ -27,7 +27,7 @@ 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"})
+          "DSP", "GameList", "FifoPlayer", "AutoUpdate", "Movie", "Input"})
     {
       if (config_location.section == section)
         return true;
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index 445b93132a..7eb61e86e3 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);
-  SaveInputSettings(ini);
   SaveBluetoothPassthroughSettings(ini);
   SaveUSBPassthroughSettings(ini);
   SaveJitDebugSettings(ini);
@@ -198,13 +197,6 @@ void SConfig::SaveCoreSettings(IniFile& ini)
   core->Set("CustomRTCValue", m_customRTCValue);
 }
 
-void SConfig::SaveInputSettings(IniFile& ini)
-{
-  IniFile::Section* input = ini.GetOrCreateSection("Input");
-
-  input->Set("BackgroundInput", m_BackgroundInput);
-}
-
 void SConfig::SaveBluetoothPassthroughSettings(IniFile& ini)
 {
   IniFile::Section* section = ini.GetOrCreateSection("BluetoothPassthrough");
@@ -256,7 +248,6 @@ void SConfig::LoadSettings()
   LoadGeneralSettings(ini);
   LoadInterfaceSettings(ini);
   LoadCoreSettings(ini);
-  LoadInputSettings(ini);
   LoadBluetoothPassthroughSettings(ini);
   LoadUSBPassthroughSettings(ini);
   LoadJitDebugSettings(ini);
@@ -368,13 +359,6 @@ void SConfig::LoadCoreSettings(IniFile& ini)
   core->Get("CustomRTCValue", &m_customRTCValue, 946684800);
 }
 
-void SConfig::LoadInputSettings(IniFile& ini)
-{
-  IniFile::Section* input = ini.GetOrCreateSection("Input");
-
-  input->Get("BackgroundInput", &m_BackgroundInput, false);
-}
-
 void SConfig::LoadBluetoothPassthroughSettings(IniFile& ini)
 {
   IniFile::Section* section = ini.GetOrCreateSection("BluetoothPassthrough");
diff --git a/Source/Core/Core/ConfigManager.h b/Source/Core/Core/ConfigManager.h
index 65540cad46..3dc1e285d0 100644
--- a/Source/Core/Core/ConfigManager.h
+++ b/Source/Core/Core/ConfigManager.h
@@ -230,7 +230,6 @@ struct SConfig
   bool m_PauseOnFocusLost;
 
   // Input settings
-  bool m_BackgroundInput;
   bool m_AdapterRumble[4];
   bool m_AdapterKonga[4];
 
@@ -257,7 +256,6 @@ private:
   void SaveGeneralSettings(IniFile& ini);
   void SaveInterfaceSettings(IniFile& ini);
   void SaveCoreSettings(IniFile& ini);
-  void SaveInputSettings(IniFile& ini);
   void SaveBluetoothPassthroughSettings(IniFile& ini);
   void SaveUSBPassthroughSettings(IniFile& ini);
   void SaveJitDebugSettings(IniFile& ini);
@@ -265,7 +263,6 @@ private:
   void LoadGeneralSettings(IniFile& ini);
   void LoadInterfaceSettings(IniFile& ini);
   void LoadCoreSettings(IniFile& ini);
-  void LoadInputSettings(IniFile& ini);
   void LoadBluetoothPassthroughSettings(IniFile& ini);
   void LoadUSBPassthroughSettings(IniFile& ini);
   void LoadJitDebugSettings(IniFile& ini);
diff --git a/Source/Core/Core/HW/VideoInterface.cpp b/Source/Core/Core/HW/VideoInterface.cpp
index bad83c9bc2..075484b315 100644
--- a/Source/Core/Core/HW/VideoInterface.cpp
+++ b/Source/Core/Core/HW/VideoInterface.cpp
@@ -881,7 +881,7 @@ void Update(u64 ticks)
 
   if (s_half_line_of_next_si_poll == s_half_line_count)
   {
-    Core::UpdateInputGate(!SConfig::GetInstance().m_BackgroundInput,
+    Core::UpdateInputGate(!Config::Get(Config::MAIN_INPUT_BACKGROUND_INPUT),
                           SConfig::GetInstance().bLockCursor);
     SerialInterface::UpdateDevices();
     s_half_line_of_next_si_poll += 2 * SerialInterface::GetPollXLines();
diff --git a/Source/Core/DolphinQt/Config/CommonControllersWidget.cpp b/Source/Core/DolphinQt/Config/CommonControllersWidget.cpp
index 2eb5b0ef37..fc70a2b505 100644
--- a/Source/Core/DolphinQt/Config/CommonControllersWidget.cpp
+++ b/Source/Core/DolphinQt/Config/CommonControllersWidget.cpp
@@ -8,7 +8,7 @@
 #include <QPushButton>
 #include <QVBoxLayout>
 
-#include "Core/ConfigManager.h"
+#include "Core/Config/MainSettings.h"
 #include "Core/Core.h"
 
 #include "DolphinQt/Config/ControllerInterface/ControllerInterfaceWindow.h"
@@ -57,11 +57,11 @@ void CommonControllersWidget::OnControllerInterfaceConfigure()
 
 void CommonControllersWidget::LoadSettings()
 {
-  m_common_bg_input->setChecked(SConfig::GetInstance().m_BackgroundInput);
+  m_common_bg_input->setChecked(Config::Get(Config::MAIN_INPUT_BACKGROUND_INPUT));
 }
 
 void CommonControllersWidget::SaveSettings()
 {
-  SConfig::GetInstance().m_BackgroundInput = m_common_bg_input->isChecked();
-  SConfig::GetInstance().SaveSettings();
+  Config::SetBaseOrCurrent(Config::MAIN_INPUT_BACKGROUND_INPUT, m_common_bg_input->isChecked());
+  Config::Save();
 }
diff --git a/Source/Core/DolphinQt/RenderWidget.cpp b/Source/Core/DolphinQt/RenderWidget.cpp
index b62a097a2f..c97814a2f1 100644
--- a/Source/Core/DolphinQt/RenderWidget.cpp
+++ b/Source/Core/DolphinQt/RenderWidget.cpp
@@ -157,7 +157,7 @@ void RenderWidget::UpdateCursor()
     const bool keep_on_top = (windowFlags() & Qt::WindowStaysOnTopHint) != 0;
     const bool should_hide =
         (Settings::Instance().GetCursorVisibility() == SConfig::ShowCursor::Never) &&
-        (keep_on_top || SConfig::GetInstance().m_BackgroundInput || isActiveWindow());
+        (keep_on_top || Config::Get(Config::MAIN_INPUT_BACKGROUND_INPUT) || isActiveWindow());
     setCursor(should_hide ? Qt::BlankCursor : Qt::ArrowCursor);
   }
   else