diff --git a/src/yuzu/hotkeys.cpp b/src/yuzu/hotkeys.cpp
index 6530186c10..2b87b999ee 100644
--- a/src/yuzu/hotkeys.cpp
+++ b/src/yuzu/hotkeys.cpp
@@ -181,6 +181,10 @@ bool ControllerShortcut::IsEnabled() const {
     return is_enabled;
 }
 
+bool ControllerShortcut::IsActive() const {
+    return active;
+}
+
 void ControllerShortcut::ControllerUpdateEvent(Core::HID::ControllerTriggerType type) {
     if (!is_enabled) {
         return;
diff --git a/src/yuzu/hotkeys.h b/src/yuzu/hotkeys.h
index 56eee8d821..bfe1f19177 100644
--- a/src/yuzu/hotkeys.h
+++ b/src/yuzu/hotkeys.h
@@ -39,6 +39,7 @@ public:
 
     void SetEnabled(bool enable);
     bool IsEnabled() const;
+    bool IsActive() const;
 
 Q_SIGNALS:
     void Activated();
diff --git a/src/yuzu/main.cpp b/src/yuzu/main.cpp
index 1431cf2fee..fddfc3d699 100644
--- a/src/yuzu/main.cpp
+++ b/src/yuzu/main.cpp
@@ -3449,7 +3449,19 @@ void GMainWindow::OnStopGame() {
 }
 
 bool GMainWindow::ConfirmShutdownGame() {
-    if (UISettings::values.confirm_before_stopping.GetValue() == ConfirmStop::Ask_Always) {
+    static const QString main_window = QStringLiteral("Main Window");
+    static const QString action = QStringLiteral("Stop Emulation");
+    auto* controller = system->HIDCore().GetEmulatedController(Core::HID::NpadIdType::Player1);
+    auto* hotkey = hotkey_registry.GetControllerHotkey(main_window, action, controller);
+
+    ConfirmStop confirm_action = UISettings::values.confirm_before_stopping.GetValue();
+
+    // Always ask when using the controller hotkey
+    if (hotkey != nullptr && hotkey->IsActive()) {
+        confirm_action = ConfirmStop::Ask_Always;
+    }
+
+    if (confirm_action == ConfirmStop::Ask_Always) {
         if (system->GetExitLocked()) {
             if (!ConfirmForceLockedExit()) {
                 return false;
@@ -3459,13 +3471,9 @@ bool GMainWindow::ConfirmShutdownGame() {
                 return false;
             }
         }
-    } else {
-        if (UISettings::values.confirm_before_stopping.GetValue() ==
-                ConfirmStop::Ask_Based_On_Game &&
-            system->GetExitLocked()) {
-            if (!ConfirmForceLockedExit()) {
-                return false;
-            }
+    } else if (confirm_action == ConfirmStop::Ask_Based_On_Game && system->GetExitLocked()) {
+        if (!ConfirmForceLockedExit()) {
+            return false;
         }
     }
     return true;
diff --git a/src/yuzu/uisettings.h b/src/yuzu/uisettings.h
index b62ff620ce..6a3f215865 100644
--- a/src/yuzu/uisettings.h
+++ b/src/yuzu/uisettings.h
@@ -98,7 +98,7 @@ struct Values {
         true,    true};
 
     SwitchableSetting<ConfirmStop> confirm_before_stopping{linkage,
-                                                           ConfirmStop::Ask_Always,
+                                                           ConfirmStop::Ask_Based_On_Game,
                                                            "confirmStop",
                                                            Category::UiGeneral,
                                                            Settings::Specialization::Default,