diff --git a/src/common/settings.h b/src/common/settings.h
index 4d0694b7d..512ecff69 100644
--- a/src/common/settings.h
+++ b/src/common/settings.h
@@ -482,7 +482,7 @@ struct Values {
     SwitchableSetting<s32, true> sound_index{1, 0, 2, "sound_index"};
 
     // Controls
-    InputSetting<std::array<PlayerInput, 8>> players;
+    InputSetting<std::array<PlayerInput, 10>> players;
 
     SwitchableSetting<bool> use_docked_mode{true, "use_docked_mode"};
 
diff --git a/src/core/hid/emulated_controller.cpp b/src/core/hid/emulated_controller.cpp
index 9f0ceca49..a29c9a6f8 100644
--- a/src/core/hid/emulated_controller.cpp
+++ b/src/core/hid/emulated_controller.cpp
@@ -82,12 +82,7 @@ Settings::ControllerType EmulatedController::MapNPadToSettingsType(NpadStyleInde
 }
 
 void EmulatedController::ReloadFromSettings() {
-    if (npad_id_type == NpadIdType::Other) {
-        ReloadDebugPadFromSettings();
-        return;
-    }
-
-    const auto player_index = NpadIdTypeToConfigIndex(npad_id_type);
+    const auto player_index = NpadIdTypeToIndex(npad_id_type);
     const auto& player = Settings::values.players.GetValue()[player_index];
 
     for (std::size_t index = 0; index < player.buttons.size(); ++index) {
@@ -116,21 +111,13 @@ void EmulatedController::ReloadFromSettings() {
 
     ring_params[0] = Common::ParamPackage(Settings::values.ringcon_analogs);
 
-    SetNpadStyleIndex(MapSettingsTypeToNPad(player.controller_type));
-    original_npad_type = npad_type;
-
-    // Player 1 shares config with handheld. Disable controller when handheld is selected
-    if (npad_id_type == NpadIdType::Player1 && npad_type == NpadStyleIndex::Handheld) {
-        Disconnect();
-        ReloadInput();
-        return;
-    }
-
-    // Handheld shares config with player 1. Disable controller when handheld isn't selected
-    if (npad_id_type == NpadIdType::Handheld && npad_type != NpadStyleIndex::Handheld) {
-        Disconnect();
-        ReloadInput();
-        return;
+    // Other or debug controller should always be a pro controller
+    if (npad_id_type != NpadIdType::Other) {
+        SetNpadStyleIndex(MapSettingsTypeToNPad(player.controller_type));
+        original_npad_type = npad_type;
+    } else {
+        SetNpadStyleIndex(NpadStyleIndex::ProController);
+        original_npad_type = npad_type;
     }
 
     Disconnect();
@@ -141,33 +128,6 @@ void EmulatedController::ReloadFromSettings() {
     ReloadInput();
 }
 
-void EmulatedController::ReloadDebugPadFromSettings() {
-    for (std::size_t index = 0; index < Settings::values.debug_pad_buttons.size(); ++index) {
-        button_params[index] = Common::ParamPackage(Settings::values.debug_pad_buttons[index]);
-    }
-    for (std::size_t index = 0; index < Settings::values.debug_pad_analogs.size(); ++index) {
-        stick_params[index] = Common::ParamPackage(Settings::values.debug_pad_analogs[index]);
-    }
-    for (std::size_t index = 0; index < motion_params.size(); ++index) {
-        motion_params[index] = {};
-    }
-
-    controller.color_values = {};
-    controller.colors_state.fullkey = {};
-    controller.colors_state.left = {};
-    controller.colors_state.right = {};
-    ring_params[0] = {};
-    SetNpadStyleIndex(NpadStyleIndex::ProController);
-    original_npad_type = npad_type;
-
-    Disconnect();
-    if (Settings::values.debug_pad_enabled) {
-        Connect();
-    }
-
-    ReloadInput();
-}
-
 void EmulatedController::LoadDevices() {
     // TODO(german77): Use more buttons to detect the correct device
     const auto left_joycon = button_params[Settings::NativeButton::DRight];
@@ -600,23 +560,9 @@ bool EmulatedController::IsConfiguring() const {
 }
 
 void EmulatedController::SaveCurrentConfig() {
-    // Other can't alter the config from here
-    if (npad_id_type == NpadIdType::Other) {
-        return;
-    }
-
-    const auto player_index = NpadIdTypeToConfigIndex(npad_id_type);
+    const auto player_index = NpadIdTypeToIndex(npad_id_type);
     auto& player = Settings::values.players.GetValue()[player_index];
-
-    // Only save the connected status when handheld is connected
-    if (npad_id_type == NpadIdType::Handheld && npad_type == NpadStyleIndex::Handheld) {
-        player.connected = is_connected;
-    }
-
-    if (npad_id_type != NpadIdType::Handheld && npad_type != NpadStyleIndex::Handheld) {
-        player.connected = is_connected;
-    }
-
+    player.connected = is_connected;
     player.controller_type = MapNPadToSettingsType(npad_type);
     for (std::size_t index = 0; index < player.buttons.size(); ++index) {
         player.buttons[index] = button_params[index].Serialize();
@@ -1206,7 +1152,7 @@ bool EmulatedController::SetVibration(std::size_t device_index, VibrationValue v
     if (!output_devices[device_index]) {
         return false;
     }
-    const auto player_index = NpadIdTypeToConfigIndex(npad_id_type);
+    const auto player_index = NpadIdTypeToIndex(npad_id_type);
     const auto& player = Settings::values.players.GetValue()[player_index];
     const f32 strength = static_cast<f32>(player.vibration_strength) / 100.0f;
 
@@ -1232,7 +1178,7 @@ bool EmulatedController::SetVibration(std::size_t device_index, VibrationValue v
 }
 
 bool EmulatedController::IsVibrationEnabled(std::size_t device_index) {
-    const auto player_index = NpadIdTypeToConfigIndex(npad_id_type);
+    const auto player_index = NpadIdTypeToIndex(npad_id_type);
     const auto& player = Settings::values.players.GetValue()[player_index];
 
     if (!player.vibration_enabled) {
diff --git a/src/core/hid/emulated_controller.h b/src/core/hid/emulated_controller.h
index 99572b3bd..a9da465a2 100644
--- a/src/core/hid/emulated_controller.h
+++ b/src/core/hid/emulated_controller.h
@@ -250,14 +250,9 @@ public:
     /// Reload all input devices
     void ReloadInput();
 
-    /// Overrides current mapped devices with the stored configuration and reloads all input
-    /// callbacks
+    /// Overrides current mapped devices with the stored configuration and reloads all input devices
     void ReloadFromSettings();
 
-    /// Overrides current mapped debug pad with the stored configuration and reloads all input
-    /// callbacks
-    void ReloadDebugPadFromSettings();
-
     /// Saves the current mapped configuration
     void SaveCurrentConfig();
 
diff --git a/src/core/hid/hid_types.h b/src/core/hid/hid_types.h
index 983f0addd..6b35f448c 100644
--- a/src/core/hid/hid_types.h
+++ b/src/core/hid/hid_types.h
@@ -690,32 +690,6 @@ constexpr size_t NpadIdTypeToIndex(NpadIdType npad_id_type) {
     }
 }
 
-/// Converts a NpadIdType to a config array index.
-constexpr size_t NpadIdTypeToConfigIndex(NpadIdType npad_id_type) {
-    switch (npad_id_type) {
-    case NpadIdType::Player1:
-        return 0;
-    case NpadIdType::Player2:
-        return 1;
-    case NpadIdType::Player3:
-        return 2;
-    case NpadIdType::Player4:
-        return 3;
-    case NpadIdType::Player5:
-        return 4;
-    case NpadIdType::Player6:
-        return 5;
-    case NpadIdType::Player7:
-        return 6;
-    case NpadIdType::Player8:
-        return 7;
-    case NpadIdType::Other:
-    case NpadIdType::Handheld:
-    default:
-        return 0;
-    }
-}
-
 /// Converts an array index to a NpadIdType
 constexpr NpadIdType IndexToNpadIdType(size_t index) {
     switch (index) {
diff --git a/src/yuzu/applets/qt_controller.cpp b/src/yuzu/applets/qt_controller.cpp
index d22db9f6b..c30b54499 100644
--- a/src/yuzu/applets/qt_controller.cpp
+++ b/src/yuzu/applets/qt_controller.cpp
@@ -542,14 +542,19 @@ void QtControllerSelectorDialog::UpdateControllerState(std::size_t player_index)
     const auto player_connected = player_groupboxes[player_index]->isChecked() &&
                                   controller_type != Core::HID::NpadStyleIndex::Handheld;
 
+    if (controller->GetNpadStyleIndex(true) == controller_type &&
+        controller->IsConnected(true) == player_connected) {
+        return;
+    }
+
     // Disconnect the controller first.
     UpdateController(controller, controller_type, false);
 
     // Handheld
     if (player_index == 0) {
-        auto* handheld = system.HIDCore().GetEmulatedController(Core::HID::NpadIdType::Handheld);
-        UpdateController(handheld, controller_type, false);
         if (controller_type == Core::HID::NpadStyleIndex::Handheld) {
+            auto* handheld =
+                system.HIDCore().GetEmulatedController(Core::HID::NpadIdType::Handheld);
             UpdateController(handheld, Core::HID::NpadStyleIndex::Handheld,
                              player_groupboxes[player_index]->isChecked());
         }
diff --git a/src/yuzu/configuration/config.cpp b/src/yuzu/configuration/config.cpp
index 4dad83b75..bb731276e 100644
--- a/src/yuzu/configuration/config.cpp
+++ b/src/yuzu/configuration/config.cpp
@@ -212,11 +212,16 @@ void Config::ReadPlayerValue(std::size_t player_index) {
     }
 
     if (player_prefix.isEmpty() && Settings::IsConfiguringGlobal()) {
-        player.controller_type = static_cast<Settings::ControllerType>(
+        const auto controller = static_cast<Settings::ControllerType>(
             qt_config
                 ->value(QStringLiteral("%1type").arg(player_prefix),
                         static_cast<u8>(Settings::ControllerType::ProController))
                 .toUInt());
+
+        if (controller == Settings::ControllerType::LeftJoycon ||
+            controller == Settings::ControllerType::RightJoycon) {
+            player.controller_type = controller;
+        }
     } else {
         player.connected =
             ReadSetting(QStringLiteral("%1connected").arg(player_prefix), player_index == 0)
diff --git a/src/yuzu/configuration/configure_input_per_game.cpp b/src/yuzu/configuration/configure_input_per_game.cpp
index 4e77fe00b..78e65d468 100644
--- a/src/yuzu/configuration/configure_input_per_game.cpp
+++ b/src/yuzu/configuration/configure_input_per_game.cpp
@@ -57,7 +57,7 @@ void ConfigureInputPerGame::ApplyConfiguration() {
 }
 
 void ConfigureInputPerGame::LoadConfiguration() {
-    static constexpr size_t HANDHELD_INDEX = 0;
+    static constexpr size_t HANDHELD_INDEX = 8;
 
     auto& hid_core = system.HIDCore();
     for (size_t player_index = 0; player_index < profile_comboboxes.size(); ++player_index) {
@@ -69,6 +69,9 @@ void ConfigureInputPerGame::LoadConfiguration() {
         const auto selection_index = player_combobox->currentIndex();
         if (selection_index == 0) {
             Settings::values.players.GetValue()[player_index].profile_name = "";
+            if (player_index == 0) {
+                Settings::values.players.GetValue()[HANDHELD_INDEX] = {};
+            }
             Settings::values.players.SetGlobal(true);
             emulated_controller->ReloadFromSettings();
             continue;
diff --git a/src/yuzu/configuration/configure_input_player.cpp b/src/yuzu/configuration/configure_input_player.cpp
index 93eb10ceb..50b62293e 100644
--- a/src/yuzu/configuration/configure_input_player.cpp
+++ b/src/yuzu/configuration/configure_input_player.cpp
@@ -1589,6 +1589,7 @@ void ConfigureInputPlayer::LoadProfile() {
 }
 
 void ConfigureInputPlayer::SaveProfile() {
+    static constexpr size_t HANDHELD_INDEX = 8;
     const QString profile_name = ui->comboProfiles->itemText(ui->comboProfiles->currentIndex());
 
     if (profile_name.isEmpty()) {
@@ -1597,7 +1598,12 @@ void ConfigureInputPlayer::SaveProfile() {
 
     ApplyConfiguration();
 
-    if (!profiles->SaveProfile(profile_name.toStdString(), player_index)) {
+    // When we're in handheld mode, only the handheld emulated controller bindings are updated
+    const bool is_handheld = player_index == 0 && emulated_controller->GetNpadIdType() ==
+                                                      Core::HID::NpadIdType::Handheld;
+    const auto profile_player_index = is_handheld ? HANDHELD_INDEX : player_index;
+
+    if (!profiles->SaveProfile(profile_name.toStdString(), profile_player_index)) {
         QMessageBox::critical(this, tr("Save Input Profile"),
                               tr("Failed to save the input profile \"%1\"").arg(profile_name));
         UpdateInputProfiles();