diff --git a/src/Ryujinx.UI.Common/Configuration/ConfigurationState.cs b/src/Ryujinx.UI.Common/Configuration/ConfigurationState.cs
index 3a88661e6..5d709d817 100644
--- a/src/Ryujinx.UI.Common/Configuration/ConfigurationState.cs
+++ b/src/Ryujinx.UI.Common/Configuration/ConfigurationState.cs
@@ -390,6 +390,11 @@ namespace Ryujinx.UI.Common.Configuration
             /// </summary>
             public ReactiveObject<bool> IgnoreMissingServices { get; private set; }
 
+            /// <summary>
+            /// Ignore Controller Applet
+            /// </summary>
+            public ReactiveObject<bool> IgnoreControllerApplet { get; private set; }
+
             /// <summary>
             /// Uses Hypervisor over JIT if available
             /// </summary>
@@ -426,6 +431,8 @@ namespace Ryujinx.UI.Common.Configuration
                 DramSize.Event += static (_, e) => LogValueChange(e, nameof(DramSize));
                 IgnoreMissingServices = new ReactiveObject<bool>();
                 IgnoreMissingServices.Event += static (_, e) => LogValueChange(e, nameof(IgnoreMissingServices));
+                IgnoreControllerApplet = new ReactiveObject<bool>();
+                IgnoreControllerApplet.Event += static (_, e) => LogValueChange(e, nameof(IgnoreControllerApplet));
                 AudioVolume = new ReactiveObject<float>();
                 AudioVolume.Event += static (_, e) => LogValueChange(e, nameof(AudioVolume));
                 UseHypervisor = new ReactiveObject<bool>();
@@ -698,11 +705,6 @@ namespace Ryujinx.UI.Common.Configuration
         /// </summary>
         public ReactiveObject<bool> ShowConfirmExit { get; private set; }
 
-        /// <summary>
-        /// Ignore Controller Applet
-        /// </summary>
-        public ReactiveObject<bool> IgnoreControllerApplet { get; private set; }
-
         /// <summary>
         /// Enables or disables save window size, position and state on close.
         /// </summary>
@@ -729,7 +731,6 @@ namespace Ryujinx.UI.Common.Configuration
             EnableDiscordIntegration = new ReactiveObject<bool>();
             CheckUpdatesOnStart = new ReactiveObject<bool>();
             ShowConfirmExit = new ReactiveObject<bool>();
-            IgnoreControllerApplet = new ReactiveObject<bool>();
             RememberWindowState = new ReactiveObject<bool>();
             EnableHardwareAcceleration = new ReactiveObject<bool>();
             HideCursor = new ReactiveObject<HideCursorMode>();
@@ -769,7 +770,6 @@ namespace Ryujinx.UI.Common.Configuration
                 EnableDiscordIntegration = EnableDiscordIntegration,
                 CheckUpdatesOnStart = CheckUpdatesOnStart,
                 ShowConfirmExit = ShowConfirmExit,
-                IgnoreApplet = IgnoreControllerApplet,
                 RememberWindowState = RememberWindowState,
                 EnableHardwareAcceleration = EnableHardwareAcceleration,
                 HideCursor = HideCursor,
@@ -791,6 +791,7 @@ namespace Ryujinx.UI.Common.Configuration
                 MemoryManagerMode = System.MemoryManagerMode,
                 DramSize = System.DramSize,
                 IgnoreMissingServices = System.IgnoreMissingServices,
+                IgnoreApplet = System.IgnoreControllerApplet,
                 UseHypervisor = System.UseHypervisor,
                 GuiColumns = new GuiColumns
                 {
@@ -889,7 +890,6 @@ namespace Ryujinx.UI.Common.Configuration
             EnableDiscordIntegration.Value = true;
             CheckUpdatesOnStart.Value = true;
             ShowConfirmExit.Value = true;
-            IgnoreControllerApplet.Value = false;
             RememberWindowState.Value = true;
             EnableHardwareAcceleration.Value = true;
             HideCursor.Value = HideCursorMode.OnIdle;
@@ -912,6 +912,7 @@ namespace Ryujinx.UI.Common.Configuration
             System.MemoryManagerMode.Value = MemoryManagerMode.HostMappedUnsafe;
             System.DramSize.Value = MemoryConfiguration.MemoryConfiguration4GiB;
             System.IgnoreMissingServices.Value = false;
+            System.IgnoreControllerApplet.Value = false;
             System.UseHypervisor.Value = true;
             Multiplayer.LanInterfaceId.Value = "0";
             Multiplayer.Mode.Value = MultiplayerMode.Disabled;
@@ -1696,7 +1697,6 @@ namespace Ryujinx.UI.Common.Configuration
             EnableDiscordIntegration.Value = configurationFileFormat.EnableDiscordIntegration;
             CheckUpdatesOnStart.Value = configurationFileFormat.CheckUpdatesOnStart;
             ShowConfirmExit.Value = configurationFileFormat.ShowConfirmExit;
-            IgnoreControllerApplet.Value = configurationFileFormat.IgnoreApplet;
             RememberWindowState.Value = configurationFileFormat.RememberWindowState;
             EnableHardwareAcceleration.Value = configurationFileFormat.EnableHardwareAcceleration;
             HideCursor.Value = configurationFileFormat.HideCursor;
@@ -1718,6 +1718,7 @@ namespace Ryujinx.UI.Common.Configuration
             System.MemoryManagerMode.Value = configurationFileFormat.MemoryManagerMode;
             System.DramSize.Value = configurationFileFormat.DramSize;
             System.IgnoreMissingServices.Value = configurationFileFormat.IgnoreMissingServices;
+            System.IgnoreControllerApplet.Value = configurationFileFormat.IgnoreApplet;
             System.UseHypervisor.Value = configurationFileFormat.UseHypervisor;
             UI.GuiColumns.FavColumn.Value = configurationFileFormat.GuiColumns.FavColumn;
             UI.GuiColumns.IconColumn.Value = configurationFileFormat.GuiColumns.IconColumn;
diff --git a/src/Ryujinx/Headless/Options.cs b/src/Ryujinx/Headless/Options.cs
index 07a4aa7d2..910267e7c 100644
--- a/src/Ryujinx/Headless/Options.cs
+++ b/src/Ryujinx/Headless/Options.cs
@@ -145,7 +145,7 @@ namespace Ryujinx.Headless
                 IgnoreMissingServices = configurationState.System.IgnoreMissingServices;
             
             if (NeedsOverride(nameof(IgnoreControllerApplet)))
-                IgnoreControllerApplet = configurationState.IgnoreControllerApplet;
+                IgnoreControllerApplet = configurationState.System.IgnoreControllerApplet;
             
             return;
 
diff --git a/src/Ryujinx/UI/Applet/AvaHostUIHandler.cs b/src/Ryujinx/UI/Applet/AvaHostUIHandler.cs
index 05207c820..c13a85d1a 100644
--- a/src/Ryujinx/UI/Applet/AvaHostUIHandler.cs
+++ b/src/Ryujinx/UI/Applet/AvaHostUIHandler.cs
@@ -33,7 +33,7 @@ namespace Ryujinx.Ava.UI.Applet
         {
             ManualResetEvent dialogCloseEvent = new(false);
 
-            bool ignoreControllerApplet = ConfigurationState.Instance.IgnoreControllerApplet;
+            bool ignoreControllerApplet = ConfigurationState.Instance.System.IgnoreControllerApplet;
             bool okPressed = false;
 
             if (ignoreControllerApplet)
diff --git a/src/Ryujinx/UI/ViewModels/SettingsViewModel.cs b/src/Ryujinx/UI/ViewModels/SettingsViewModel.cs
index e520f5c3d..7a9cce0bb 100644
--- a/src/Ryujinx/UI/ViewModels/SettingsViewModel.cs
+++ b/src/Ryujinx/UI/ViewModels/SettingsViewModel.cs
@@ -532,7 +532,6 @@ namespace Ryujinx.Ava.UI.ViewModels
             EnableDiscordIntegration = config.EnableDiscordIntegration;
             CheckUpdatesOnStart = config.CheckUpdatesOnStart;
             ShowConfirmExit = config.ShowConfirmExit;
-            IgnoreApplet = config.IgnoreControllerApplet;
             RememberWindowState = config.RememberWindowState;
             HideCursor = (int)config.HideCursor.Value;
 
@@ -577,6 +576,7 @@ namespace Ryujinx.Ava.UI.ViewModels
             EnableFsIntegrityChecks = config.System.EnableFsIntegrityChecks;
             DramSize = config.System.DramSize;
             IgnoreMissingServices = config.System.IgnoreMissingServices;
+            IgnoreApplet = config.System.IgnoreControllerApplet;
 
             // CPU
             EnablePptc = config.System.EnablePtc;
@@ -637,7 +637,6 @@ namespace Ryujinx.Ava.UI.ViewModels
             config.EnableDiscordIntegration.Value = EnableDiscordIntegration;
             config.CheckUpdatesOnStart.Value = CheckUpdatesOnStart;
             config.ShowConfirmExit.Value = ShowConfirmExit;
-            config.IgnoreControllerApplet.Value = IgnoreApplet;
             config.RememberWindowState.Value = RememberWindowState;
             config.HideCursor.Value = (HideCursorMode)HideCursor;
 
@@ -686,6 +685,7 @@ namespace Ryujinx.Ava.UI.ViewModels
             config.System.EnableFsIntegrityChecks.Value = EnableFsIntegrityChecks;
             config.System.DramSize.Value = DramSize;
             config.System.IgnoreMissingServices.Value = IgnoreMissingServices;
+            config.System.IgnoreControllerApplet.Value = IgnoreApplet;
 
             // CPU
             config.System.EnablePtc.Value = EnablePptc;