diff --git a/pcsx2/Frontend/SDLInputSource.cpp b/pcsx2/Frontend/SDLInputSource.cpp
index 8519dc6da4..9c9ba25fb3 100644
--- a/pcsx2/Frontend/SDLInputSource.cpp
+++ b/pcsx2/Frontend/SDLInputSource.cpp
@@ -358,6 +358,13 @@ bool SDLInputSource::ProcessSDLEvent(const SDL_Event* event)
 		case SDL_CONTROLLERBUTTONUP:
 			return HandleControllerButtonEvent(&event->cbutton);
 
+		case SDL_JOYAXISMOTION:
+			return HandleJoystickAxisEvent(&event->jaxis);
+
+		case SDL_JOYBUTTONDOWN:
+		case SDL_JOYBUTTONUP:
+			return HandleJoystickButtonEvent(&event->jbutton);
+
 		default:
 			return false;
 	}
@@ -425,6 +432,21 @@ bool SDLInputSource::OpenGameController(int index)
 	cd.haptic_left_right_effect = -1;
 	cd.game_controller = gcontroller;
 
+	const int num_axes = SDL_JoystickNumAxes(joystick);
+	const int num_buttons = SDL_JoystickNumButtons(joystick);
+	cd.joy_axis_used_in_gc.resize(num_axes, false);
+	cd.joy_button_used_in_gc.resize(num_buttons, false);
+	auto mark_bind = [&](SDL_GameControllerButtonBind bind){
+		if (bind.bindType == SDL_CONTROLLER_BINDTYPE_AXIS && bind.value.axis < num_axes)
+			cd.joy_axis_used_in_gc[bind.value.axis] = true;
+		if (bind.bindType == SDL_CONTROLLER_BINDTYPE_BUTTON && bind.value.button < num_buttons)
+			cd.joy_button_used_in_gc[bind.value.button] = true;
+	};
+	for (size_t i = 0; i < std::size(s_sdl_axis_names); i++)
+		mark_bind(SDL_GameControllerGetBindForAxis(gcontroller, static_cast<SDL_GameControllerAxis>(i)));
+	for (size_t i = 0; i < std::size(s_sdl_button_names); i++)
+		mark_bind(SDL_GameControllerGetBindForButton(gcontroller, static_cast<SDL_GameControllerButton>(i)));
+
 	cd.use_game_controller_rumble = (SDL_GameControllerRumble(gcontroller, 0, 0, 0) == 0);
 	if (cd.use_game_controller_rumble)
 	{
@@ -494,6 +516,11 @@ bool SDLInputSource::CloseGameController(int joystick_index)
 	return true;
 }
 
+static float NormalizeS16(s16 value)
+{
+	return static_cast<float>(value) / (value < 0 ? 32768.0f : 32767.0f);
+}
+
 bool SDLInputSource::HandleControllerAxisEvent(const SDL_ControllerAxisEvent* ev)
 {
 	auto it = GetControllerDataForJoystickId(ev->which);
@@ -501,8 +528,7 @@ bool SDLInputSource::HandleControllerAxisEvent(const SDL_ControllerAxisEvent* ev
 		return false;
 
 	const InputBindingKey key(MakeGenericControllerAxisKey(InputSourceType::SDL, it->player_id, ev->axis));
-	const float value = static_cast<float>(ev->value) / (ev->value < 0 ? 32768.0f : 32767.0f);
-	return InputManager::InvokeEvents(key, value);
+	return InputManager::InvokeEvents(key, NormalizeS16(ev->value));
 }
 
 bool SDLInputSource::HandleControllerButtonEvent(const SDL_ControllerButtonEvent* ev)
@@ -513,11 +539,35 @@ bool SDLInputSource::HandleControllerButtonEvent(const SDL_ControllerButtonEvent
 
 	const InputBindingKey key(MakeGenericControllerButtonKey(InputSourceType::SDL, it->player_id, ev->button));
 	const GenericInputBinding generic_key = (ev->button < std::size(s_sdl_generic_binding_button_mapping)) ?
-												s_sdl_generic_binding_button_mapping[ev->button] :
-                                                GenericInputBinding::Unknown;
+	                                            s_sdl_generic_binding_button_mapping[ev->button] :
+	                                            GenericInputBinding::Unknown;
 	return InputManager::InvokeEvents(key, (ev->state == SDL_PRESSED) ? 1.0f : 0.0f, generic_key);
 }
 
+bool SDLInputSource::HandleJoystickAxisEvent(const SDL_JoyAxisEvent* ev)
+{
+	auto it = GetControllerDataForJoystickId(ev->which);
+	if (it == m_controllers.end())
+		return false;
+	if (ev->axis < it->joy_axis_used_in_gc.size() && it->joy_axis_used_in_gc[ev->axis])
+		return false; // Will get handled by GC event
+	const u32 axis = ev->axis + std::size(s_sdl_axis_names); // Ensure we don't conflict with GC axes
+	const InputBindingKey key(MakeGenericControllerAxisKey(InputSourceType::SDL, it->player_id, axis));
+	return InputManager::InvokeEvents(key, NormalizeS16(ev->value));
+}
+
+bool SDLInputSource::HandleJoystickButtonEvent(const SDL_JoyButtonEvent* ev)
+{
+	auto it = GetControllerDataForJoystickId(ev->which);
+	if (it == m_controllers.end())
+		return false;
+	if (ev->button < it->joy_button_used_in_gc.size() && it->joy_button_used_in_gc[ev->button])
+		return false; // Will get handled by GC event
+	const u32 button = ev->button + std::size(s_sdl_button_names); // Ensure we don't conflict with GC buttons
+	const InputBindingKey key(MakeGenericControllerAxisKey(InputSourceType::SDL, it->player_id, button));
+	return InputManager::InvokeEvents(key, (ev->state == SDL_PRESSED) ? 1.0f : 0.0f);
+}
+
 std::vector<InputBindingKey> SDLInputSource::EnumerateMotors()
 {
 	std::vector<InputBindingKey> ret;
diff --git a/pcsx2/Frontend/SDLInputSource.h b/pcsx2/Frontend/SDLInputSource.h
index 65c2d6ba07..c560782521 100644
--- a/pcsx2/Frontend/SDLInputSource.h
+++ b/pcsx2/Frontend/SDLInputSource.h
@@ -47,12 +47,6 @@ public:
   bool ProcessSDLEvent(const SDL_Event* event);
 
 private:
-  enum : int
-  {
-    MAX_NUM_AXES = 7,
-    MAX_NUM_BUTTONS = 16,
-  };
-
   struct ControllerData
   {
     SDL_Haptic* haptic;
@@ -62,6 +56,10 @@ private:
     int joystick_id;
     int player_id;
     bool use_game_controller_rumble;
+
+    // Used to disable Joystick controls that are used in GameController inputs so we don't get double events
+    std::vector<bool> joy_button_used_in_gc;
+    std::vector<bool> joy_axis_used_in_gc;
   };
 
   using ControllerDataVector = std::vector<ControllerData>;
@@ -79,6 +77,8 @@ private:
   bool CloseGameController(int joystick_index);
   bool HandleControllerAxisEvent(const SDL_ControllerAxisEvent* event);
   bool HandleControllerButtonEvent(const SDL_ControllerButtonEvent* event);
+  bool HandleJoystickAxisEvent(const SDL_JoyAxisEvent* event);
+  bool HandleJoystickButtonEvent(const SDL_JoyButtonEvent* event);
   void SendRumbleUpdate(ControllerData* cd);
 
   ControllerDataVector m_controllers;