diff --git a/src/Ryujinx/Input/AutoAssignController.cs b/src/Ryujinx/Input/AutoAssignController.cs
index 58978531d..5ebba82f6 100644
--- a/src/Ryujinx/Input/AutoAssignController.cs
+++ b/src/Ryujinx/Input/AutoAssignController.cs
@@ -1,4 +1,5 @@
-using Ryujinx.Ava.UI.ViewModels;
+using Ryujinx.Ava.UI.Models.Input;
+using Ryujinx.Ava.UI.ViewModels;
 using Ryujinx.Ava.Utilities.Configuration;
 using Ryujinx.Common.Configuration.Hid;
 using Ryujinx.Common.Configuration.Hid.Controller;
@@ -61,79 +62,159 @@ namespace Ryujinx.Ava.Input
         public void RefreshControllers()
         {
             if (!_configurationState.Hid.EnableAutoAssign) return;
-            
-            // Get every controller config and update the configuration state
+
             List<IGamepad> controllers = _inputManager.GamepadDriver.GetGamepads().ToList();
             List<InputConfig> oldConfig = _configurationState.Hid.InputConfig.Value.Where(x => x != null).ToList();
-            (List<InputConfig> newConfig,  bool hasNewControllersConnected) = GetOrderedConfig(controllers, oldConfig);
-            
+
+            (List<InputConfig> newConfig, bool hasNewControllersConnected) = GetOrderedConfig(controllers, oldConfig);
+
             _viewModel.AppHost?.NpadManager.ReloadConfiguration(newConfig, _configurationState.Hid.EnableKeyboard, _configurationState.Hid.EnableMouse);
-            
-            // update the configuration state only if there are new controllers connected
-            if(hasNewControllersConnected)
+
+            if (hasNewControllersConnected)
             {
-                _configurationState.Hid.InputConfig.Value = newConfig;
                 ConfigurationState.Instance.ToFileFormat().SaveConfig(Program.ConfigurationPath);
             }
+            else
+            {
+                // we must switch the order of the controllers in oldConfig to match the new order
+                newConfig = ReorderControllers(newConfig, oldConfig);
+            }
+
+            _configurationState.Hid.InputConfig.Value = newConfig;
             ConfigurationUpdated?.Invoke();
         }
 
+        /// <summary>
+        /// Ensures that the order of controllers remains the same unless a new controller is connected.
+        /// </summary>
+        private List<InputConfig> ReorderControllers(List<InputConfig> newConfig, List<InputConfig> oldConfig)
+        {
+            List<InputConfig> reorderedConfig = oldConfig.Select(config => new GamepadInputConfig(config).GetConfig()).ToList();
+
+            foreach (var config in newConfig)
+            {
+                InputConfig substitute = reorderedConfig.FirstOrDefault(x => x.Id == config.Id);
+                InputConfig toBeReplaced = reorderedConfig.FirstOrDefault(x => x.PlayerIndex == config.PlayerIndex);
+
+                if (substitute == null || toBeReplaced == null || substitute.PlayerIndex == toBeReplaced.PlayerIndex) continue;
+
+                (substitute.PlayerIndex, toBeReplaced.PlayerIndex) = (toBeReplaced.PlayerIndex, substitute.PlayerIndex);
+            }
+
+            return reorderedConfig;
+        }
+
+        /// <summary>
+        /// Orders controllers, preserving existing mappings while assigning new controllers to available slots.
+        /// </summary>
         private (List<InputConfig>, bool) GetOrderedConfig(List<IGamepad> controllers, List<InputConfig> oldConfig)
-        { 
-            Dictionary<string, InputConfig> oldConfigMap = oldConfig.Where(c => c?.Id != null).ToDictionary(x => x.Id);
+        {
+            Dictionary<string, InputConfig> oldConfigMap = oldConfig.Where(c => c?.Id != null)
+                .ToDictionary(x => x.Id);
+
             Dictionary<int, InputConfig> playerIndexMap = new();
             HashSet<int> usedIndices = new();
             int recognizedControllersCount = 0;
 
-            // Assign controllers that have an old config
             List<IGamepad> remainingControllers = controllers.Where(c => c?.Id != null).ToList();
-            foreach (var controller in remainingControllers.ToList())
+
+            // Assign controllers that have an existing configuration
+            AssignExistingControllers(remainingControllers, oldConfigMap, playerIndexMap, usedIndices, ref recognizedControllersCount);
+
+            // Assign new controllers
+            AssignNewControllers(remainingControllers, playerIndexMap, usedIndices);
+
+            List<InputConfig> orderedConfigs = playerIndexMap.OrderBy(x => x.Key).Select(x => x.Value).ToList();
+
+            // Sequentially update PlayerIndex and LED colors
+            UpdatePlayerIndicesAndLEDs(orderedConfigs);
+
+            bool hasNewControllersConnected = controllers.Count > recognizedControllersCount;
+            return (orderedConfigs, hasNewControllersConnected);
+        }
+
+        /// <summary>
+        /// Assigns controllers with existing configurations while keeping their PlayerIndex if available.
+        /// </summary>
+        private void AssignExistingControllers(
+            List<IGamepad> controllers,
+            Dictionary<string, InputConfig> oldConfigMap,
+            Dictionary<int, InputConfig> playerIndexMap,
+            HashSet<int> usedIndices,
+            ref int recognizedControllersCount)
+        {
+            foreach (var controller in controllers.ToList())
             {
                 if (oldConfigMap.TryGetValue(controller.Id, out InputConfig existingConfig))
                 {
                     int desiredIndex = (int)existingConfig.PlayerIndex;
-                    // Check if the desired index is valid and available
+
+                    // Ensure the index is valid and available
                     if (desiredIndex < 0 || desiredIndex >= MaxControllers || usedIndices.Contains(desiredIndex))
                     {
-                        // Find the first available index
-                        desiredIndex = Enumerable.Range(0, MaxControllers).First(i => !usedIndices.Contains(i));
+                        desiredIndex = GetFirstAvailableIndex(usedIndices);
                     }
-                    existingConfig.PlayerIndex = (PlayerIndex)desiredIndex;
+
+                    InputConfig config = new GamepadInputConfig(existingConfig).GetConfig();
+                    config.PlayerIndex = (PlayerIndex)desiredIndex;
                     usedIndices.Add(desiredIndex);
-                    playerIndexMap[desiredIndex] = existingConfig;
+                    playerIndexMap[desiredIndex] = config;
                     recognizedControllersCount++;
-                    
-                    remainingControllers.Remove(controller);
+
+                    controllers.Remove(controller);
                 }
             }
+        }
 
-            // Assign remaining (new) controllers
-            foreach (var controller in remainingControllers.OrderBy(c => c.Id))
+        /// <summary>
+        /// Assigns new controllers to the first available PlayerIndex.
+        /// </summary>
+        private void AssignNewControllers(
+            List<IGamepad> controllers,
+            Dictionary<int, InputConfig> playerIndexMap,
+            HashSet<int> usedIndices)
+        {
+            foreach (var controller in controllers)
             {
                 InputConfig config = CreateConfigFromController(controller);
-                int freeIndex = Enumerable.Range(0, MaxControllers).First(i => !usedIndices.Contains(i));
+                int freeIndex = GetFirstAvailableIndex(usedIndices);
                 config.PlayerIndex = (PlayerIndex)freeIndex;
                 usedIndices.Add(freeIndex);
                 playerIndexMap[freeIndex] = config;
             }
+        }
 
-            List<InputConfig> orderedConfigs = playerIndexMap.OrderBy(x => x.Key).Select(x => x.Value).ToList();
-
-            // Sequential reassignment of PlayerIndex and LED colors
-            int index = 0;
-            foreach (var config in orderedConfigs)
+        /// <summary>
+        /// Finds the first available PlayerIndex that isn't in use.
+        /// </summary>
+        private int GetFirstAvailableIndex(HashSet<int> usedIndices)
+        {
+            for (int i = 0; i < MaxControllers; i++)
             {
-                config.PlayerIndex = (PlayerIndex)index;
-                if (config is StandardControllerInputConfig standardConfig)
-                {
-                    Logger.Warning?.Print(LogClass.Application, $"Setting color for Player{index+1}");
-                    standardConfig.Led = new LedConfigController { EnableLed = true, LedColor = _playerColors[index] };
-                }
-                index++;
+                if (!usedIndices.Contains(i)) return i;
             }
+            return -1; // Should not happen unless MaxControllers is exceeded
+        }
 
-            bool hasNewControllersConnected = (controllers.Count > recognizedControllersCount);
-            return (orderedConfigs, hasNewControllersConnected);
+        /// <summary>
+        /// Updates PlayerIndex and LED configurations sequentially.
+        /// </summary>
+        private void UpdatePlayerIndicesAndLEDs(List<InputConfig> orderedConfigs)
+        {
+            for (int index = 0; index < orderedConfigs.Count; index++)
+            {
+                orderedConfigs[index].PlayerIndex = (PlayerIndex)index;
+
+                if (orderedConfigs[index] is StandardControllerInputConfig standardConfig)
+                {
+                    Logger.Warning?.Print(LogClass.Application, $"Setting color for Player{index + 1}");
+                    standardConfig.Led = new LedConfigController
+                    {
+                        EnableLed = true,
+                        LedColor = _playerColors[index]
+                    };
+                }
+            }
         }
 
         private static InputConfig CreateConfigFromController(IGamepad controller)