diff --git a/src/qt_gui/control_settings.cpp b/src/qt_gui/control_settings.cpp
index 89abcc7f4..fbeedc802 100644
--- a/src/qt_gui/control_settings.cpp
+++ b/src/qt_gui/control_settings.cpp
@@ -8,13 +8,13 @@
 #include "common/logging/log.h"
 #include "common/path_util.h"
 #include "control_settings.h"
-#include "sdl_window.h"
+#include "input/input_handler.h"
 #include "ui_control_settings.h"
 
 ControlSettings::ControlSettings(std::shared_ptr<GameInfoClass> game_info_get, bool isGameRunning,
-                                 QWidget* parent)
+                                 std::string GameRunningSerial, QWidget* parent)
     : QDialog(parent), m_game_info(game_info_get), GameRunning(isGameRunning),
-      ui(new Ui::ControlSettings) {
+      RunningGameSerial(GameRunningSerial), ui(new Ui::ControlSettings) {
 
     ui->setupUi(this);
 
@@ -24,9 +24,6 @@ ControlSettings::ControlSettings(std::shared_ptr<GameInfoClass> game_info_get, b
         CheckGamePad();
     } else {
         SDL_SetHint(SDL_HINT_JOYSTICK_ALLOW_BACKGROUND_EVENTS, "1");
-        SDL_Event pauseGame{};
-        pauseGame.type = SDL_EVENT_TOGGLE_PAUSE;
-        SDL_PushEvent(&pauseGame);
     }
 
     AddBoxItems();
@@ -327,6 +324,11 @@ void ControlSettings::SaveControllerConfig(bool CloseOnSave) {
                                      ui->BSlider->value());
     Config::save(Common::FS::GetUserPath(Common::FS::PathType::UserDir) / "config.toml");
 
+    if (GameRunning) {
+        Config::GetUseUnifiedInputConfig() ? Input::ParseInputConfig("default")
+                                           : Input::ParseInputConfig(RunningGameSerial);
+    }
+
     if (CloseOnSave)
         QWidget::close();
 }
@@ -929,9 +931,6 @@ void ControlSettings::Cleanup() {
         SDL_Quit();
     } else {
         SDL_SetHint(SDL_HINT_JOYSTICK_ALLOW_BACKGROUND_EVENTS, "0");
-        SDL_Event resumeGame{};
-        resumeGame.type = SDL_EVENT_TOGGLE_PAUSE;
-        SDL_PushEvent(&resumeGame);
     }
 }
 
diff --git a/src/qt_gui/control_settings.h b/src/qt_gui/control_settings.h
index e47a79936..00ac202fd 100644
--- a/src/qt_gui/control_settings.h
+++ b/src/qt_gui/control_settings.h
@@ -15,7 +15,7 @@ class ControlSettings : public QDialog {
     Q_OBJECT
 public:
     explicit ControlSettings(std::shared_ptr<GameInfoClass> game_info_get, bool GameRunning,
-                             QWidget* parent = nullptr);
+                             std::string GameRunningSerial, QWidget* parent = nullptr);
     ~ControlSettings();
 
 signals:
@@ -50,6 +50,7 @@ private:
     QList<QPushButton*> AxisList;
     QSet<QString> pressedButtons;
 
+    std::string RunningGameSerial;
     bool GameRunning;
     bool L2Pressed = false;
     bool R2Pressed = false;
diff --git a/src/qt_gui/kbm_gui.cpp b/src/qt_gui/kbm_gui.cpp
index 10c08e391..a67c02ff8 100644
--- a/src/qt_gui/kbm_gui.cpp
+++ b/src/qt_gui/kbm_gui.cpp
@@ -10,29 +10,23 @@
 #include <SDL3/SDL_events.h>
 
 #include "common/path_util.h"
+#include "input/input_handler.h"
 #include "kbm_config_dialog.h"
 #include "kbm_gui.h"
 #include "kbm_help_dialog.h"
-#include "sdl_window.h"
 #include "ui_kbm_gui.h"
 
 HelpDialog* HelpWindow;
 KBMSettings::KBMSettings(std::shared_ptr<GameInfoClass> game_info_get, bool isGameRunning,
-                         QWidget* parent)
+                         std::string GameRunningSerial, QWidget* parent)
     : QDialog(parent), m_game_info(game_info_get), GameRunning(isGameRunning),
-      ui(new Ui::KBMSettings) {
+      RunningGameSerial(GameRunningSerial), ui(new Ui::KBMSettings) {
 
     ui->setupUi(this);
     ui->PerGameCheckBox->setChecked(!Config::GetUseUnifiedInputConfig());
     ui->TextEditorButton->setFocus();
     this->setFocusPolicy(Qt::StrongFocus);
 
-    if (GameRunning) {
-        SDL_Event pauseGame{};
-        pauseGame.type = SDL_EVENT_TOGGLE_PAUSE;
-        SDL_PushEvent(&pauseGame);
-    }
-
     ui->MouseJoystickBox->addItem("none");
     ui->MouseJoystickBox->addItem("right");
     ui->MouseJoystickBox->addItem("left");
@@ -340,6 +334,11 @@ QString(tr("Cannot bind any unique input more than once. Duplicate inputs mapped
     Config::SetUseUnifiedInputConfig(!ui->PerGameCheckBox->isChecked());
     Config::save(Common::FS::GetUserPath(Common::FS::PathType::UserDir) / "config.toml");
 
+    if (GameRunning) {
+        Config::GetUseUnifiedInputConfig() ? Input::ParseInputConfig("default")
+                                           : Input::ParseInputConfig(RunningGameSerial);
+    }
+
     if (close_on_save)
         QWidget::close();
 }
@@ -1011,12 +1010,4 @@ bool KBMSettings::eventFilter(QObject* obj, QEvent* event) {
     return QDialog::eventFilter(obj, event);
 }
 
-void KBMSettings::Cleanup() {
-    if (GameRunning) {
-        SDL_Event resumeGame{};
-        resumeGame.type = SDL_EVENT_TOGGLE_PAUSE;
-        SDL_PushEvent(&resumeGame);
-    }
-}
-
 KBMSettings::~KBMSettings() {}
diff --git a/src/qt_gui/kbm_gui.h b/src/qt_gui/kbm_gui.h
index ddc2b9422..7a0a5916f 100644
--- a/src/qt_gui/kbm_gui.h
+++ b/src/qt_gui/kbm_gui.h
@@ -24,7 +24,7 @@ class KBMSettings : public QDialog {
     Q_OBJECT
 public:
     explicit KBMSettings(std::shared_ptr<GameInfoClass> game_info_get, bool GameRunning,
-                         QWidget* parent = nullptr);
+                         std::string GameRunningSerial, QWidget* parent = nullptr);
     ~KBMSettings();
 
 private Q_SLOTS:
@@ -47,6 +47,7 @@ private:
     void SetMapping(QString input);
     void Cleanup();
 
+    std::string RunningGameSerial;
     QSet<QString> pressedKeys;
     bool GameRunning;
     bool EnableMapping = false;
@@ -69,9 +70,4 @@ private:
 
         "pad_left",     "pad_right", "axis_left_x", "axis_left_y", "axis_right_x",
         "axis_right_y", "back"};
-
-protected:
-    void closeEvent(QCloseEvent* event) override {
-        Cleanup();
-    }
 };
diff --git a/src/qt_gui/main_window.cpp b/src/qt_gui/main_window.cpp
index 0b2b1e7cd..f561bf392 100644
--- a/src/qt_gui/main_window.cpp
+++ b/src/qt_gui/main_window.cpp
@@ -473,12 +473,13 @@ void MainWindow::CreateConnects() {
     });
 
     connect(ui->controllerButton, &QPushButton::clicked, this, [this]() {
-        ControlSettings* remapWindow = new ControlSettings(m_game_info, isGameRunning, this);
+        ControlSettings* remapWindow =
+            new ControlSettings(m_game_info, isGameRunning, runningGameSerial, this);
         remapWindow->exec();
     });
 
     connect(ui->keyboardButton, &QPushButton::clicked, this, [this]() {
-        auto kbmWindow = new KBMSettings(m_game_info, isGameRunning, this);
+        auto kbmWindow = new KBMSettings(m_game_info, isGameRunning, runningGameSerial, this);
         kbmWindow->exec();
     });
 
@@ -846,12 +847,14 @@ void MainWindow::StartGame() {
         if (m_game_list_frame->currentItem()) {
             int itemID = m_game_list_frame->currentItem()->row();
             Common::FS::PathToQString(gamePath, m_game_info->m_games[itemID].path / "eboot.bin");
+            runningGameSerial = m_game_info->m_games[itemID].serial;
         }
     } else if (table_mode == 1) {
         if (m_game_grid_frame->cellClicked) {
             int itemID = (m_game_grid_frame->crtRow * m_game_grid_frame->columnCnt) +
                          m_game_grid_frame->crtColumn;
             Common::FS::PathToQString(gamePath, m_game_info->m_games[itemID].path / "eboot.bin");
+            runningGameSerial = m_game_info->m_games[itemID].serial;
         }
     } else {
         if (m_elf_viewer->currentItem()) {
diff --git a/src/qt_gui/main_window.h b/src/qt_gui/main_window.h
index eec1a65de..5b880c15e 100644
--- a/src/qt_gui/main_window.h
+++ b/src/qt_gui/main_window.h
@@ -75,11 +75,13 @@ private:
     void PlayBackgroundMusic();
     QIcon RecolorIcon(const QIcon& icon, bool isWhite);
     void StartEmulator(std::filesystem::path);
+
     bool isIconBlack = false;
     bool isTableList = true;
     bool isGameRunning = false;
     bool isWhite = false;
     bool is_paused = false;
+    std::string runningGameSerial = "";
 
     QActionGroup* m_icon_size_act_group = nullptr;
     QActionGroup* m_list_mode_act_group = nullptr;
diff --git a/src/qt_gui/sdl_event_wrapper.cpp b/src/qt_gui/sdl_event_wrapper.cpp
index c45d4d448..3f6ba6e93 100644
--- a/src/qt_gui/sdl_event_wrapper.cpp
+++ b/src/qt_gui/sdl_event_wrapper.cpp
@@ -19,6 +19,10 @@ Wrapper* Wrapper::GetInstance() {
 
 bool Wrapper::ProcessEvent(SDL_Event* event) {
     switch (event->type) {
+    case SDL_EVENT_GAMEPAD_ADDED:
+        return false;
+    case SDL_EVENT_GAMEPAD_REMOVED:
+        return false;
     case SDL_EVENT_QUIT:
         emit SDLEvent(SDL_EVENT_QUIT, 0, 0);
         return true;
@@ -31,8 +35,9 @@ bool Wrapper::ProcessEvent(SDL_Event* event) {
     case SDL_EVENT_GAMEPAD_AXIS_MOTION:
         emit SDLEvent(SDL_EVENT_GAMEPAD_AXIS_MOTION, event->gaxis.axis, event->gaxis.value);
         return true;
+    // block all other SDL events while wrapper is active
     default:
-        return false;
+        return true;
     }
 }
 Wrapper::~Wrapper() {}