diff --git a/src/input_common/sdl/sdl_impl.cpp b/src/input_common/sdl/sdl_impl.cpp
index a9f7e51036..6024ed97a8 100644
--- a/src/input_common/sdl/sdl_impl.cpp
+++ b/src/input_common/sdl/sdl_impl.cpp
@@ -1068,7 +1068,6 @@ public:
 
     void Start(const std::string& device_id) override {
         SDLPoller::Start(device_id);
-        // Load the game controller
         // Reset stored axes
         analog_x_axis = -1;
         analog_y_axis = -1;
@@ -1081,40 +1080,21 @@ public:
             if (event.type == SDL_JOYAXISMOTION && std::abs(event.jaxis.value / 32767.0) < 0.5) {
                 continue;
             }
-            // Simplify controller config by testing if game controller support is enabled.
             if (event.type == SDL_JOYAXISMOTION) {
                 const auto axis = event.jaxis.axis;
-                if (const auto joystick = state.GetSDLJoystickBySDLID(event.jaxis.which);
-                    auto* const controller = joystick->GetSDLGameController()) {
-                    const auto axis_left_x =
-                        SDL_GameControllerGetBindForAxis(controller, SDL_CONTROLLER_AXIS_LEFTX)
-                            .value.axis;
-                    const auto axis_left_y =
-                        SDL_GameControllerGetBindForAxis(controller, SDL_CONTROLLER_AXIS_LEFTY)
-                            .value.axis;
-                    const auto axis_right_x =
-                        SDL_GameControllerGetBindForAxis(controller, SDL_CONTROLLER_AXIS_RIGHTX)
-                            .value.axis;
-                    const auto axis_right_y =
-                        SDL_GameControllerGetBindForAxis(controller, SDL_CONTROLLER_AXIS_RIGHTY)
-                            .value.axis;
-
-                    if (axis == axis_left_x || axis == axis_left_y) {
-                        analog_x_axis = axis_left_x;
-                        analog_y_axis = axis_left_y;
-                        break;
-                    } else if (axis == axis_right_x || axis == axis_right_y) {
-                        analog_x_axis = axis_right_x;
-                        analog_y_axis = axis_right_y;
-                        break;
-                    }
+                // In order to return a complete analog param, we need inputs for both axes.
+                // First we take the x-axis (horizontal) input, then the y-axis (vertical) input.
+                if (analog_x_axis == -1) {
+                    analog_x_axis = axis;
+                } else if (analog_y_axis == -1 && analog_x_axis != axis) {
+                    analog_y_axis = axis;
+                }
+            } else {
+                // If the press wasn't accepted as a joy axis, check for a button press
+                auto button_press = button_poller.FromEvent(event);
+                if (button_press) {
+                    return *button_press;
                 }
-            }
-
-            // If the press wasn't accepted as a joy axis, check for a button press
-            auto button_press = button_poller.FromEvent(event);
-            if (button_press) {
-                return *button_press;
             }
         }
 
@@ -1127,6 +1107,7 @@ public:
                 return params;
             }
         }
+
         return {};
     }
 
diff --git a/src/yuzu/configuration/configure_input_player.cpp b/src/yuzu/configuration/configure_input_player.cpp
index 4ed704793c..5abf9f0bf4 100644
--- a/src/yuzu/configuration/configure_input_player.cpp
+++ b/src/yuzu/configuration/configure_input_player.cpp
@@ -370,6 +370,18 @@ ConfigureInputPlayer::ConfigureInputPlayer(QWidget* parent, std::size_t player_i
             }
 
             connect(analog_button, &QPushButton::clicked, [=, this] {
+                if (!map_analog_stick_accepted) {
+                    map_analog_stick_accepted =
+                        QMessageBox::information(
+                            this, tr("Map Analog Stick"),
+                            tr("After pressing OK, first move your joystick horizontally, and then "
+                               "vertically.\nTo invert the axes, first move your joystick "
+                               "vertically, and then horizontally."),
+                            QMessageBox::Ok | QMessageBox::Cancel) == QMessageBox::Ok;
+                    if (!map_analog_stick_accepted) {
+                        return;
+                    }
+                }
                 HandleClick(
                     analog_map_buttons[analog_id][sub_button_id],
                     [=, this](const Common::ParamPackage& params) {
diff --git a/src/yuzu/configuration/configure_input_player.h b/src/yuzu/configuration/configure_input_player.h
index 05dee5af51..4895e8850e 100644
--- a/src/yuzu/configuration/configure_input_player.h
+++ b/src/yuzu/configuration/configure_input_player.h
@@ -181,9 +181,12 @@ private:
 
     std::vector<std::unique_ptr<InputCommon::Polling::DevicePoller>> device_pollers;
 
+    /// A flag to indicate that the "Map Analog Stick" pop-up has been shown and accepted once.
+    bool map_analog_stick_accepted{};
+
     /// A flag to indicate if keyboard keys are okay when configuring an input. If this is false,
     /// keyboard events are ignored.
-    bool want_keyboard_mouse = false;
+    bool want_keyboard_mouse{};
 
     /// List of physical devices users can map with. If a SDL backed device is selected, then you
     /// can use this device to get a default mapping.