diff --git a/src/RunnerV2/RunnerV2/Helpers/SettingsHelper.cs b/src/RunnerV2/RunnerV2/Helpers/SettingsHelper.cs
index cb38e4b40e..492dbb29be 100644
--- a/src/RunnerV2/RunnerV2/Helpers/SettingsHelper.cs
+++ b/src/RunnerV2/RunnerV2/Helpers/SettingsHelper.cs
@@ -168,19 +168,6 @@ namespace RunnerV2.Helpers
                             }
                         }
 
-                        CentralizedKeyboardHookManager.RemoveAllHooksFromModule("QuickAccess");
-                        if (SettingsUtils.Default.GetSettings<GeneralSettings>().EnableQuickAccess)
-                        {
-                            CentralizedKeyboardHookManager.AddKeyboardHook("QuickAccess", SettingsUtils.Default.GetSettings<GeneralSettings>().QuickAccessShortcut, QuickAccessHelper.Show);
-                        }
-                        else
-                        {
-                            CentralizedKeyboardHookManager.RemoveAllHooksFromModule("QuickAccess");
-                            QuickAccessHelper.Stop();
-                        }
-
-                        TrayIconManager.UpdateTrayIcon();
-
                         break;
                     case "powertoys":
                         foreach (var powertoysSettingsPart in property.Value.EnumerateObject())
diff --git a/src/RunnerV2/RunnerV2/Helpers/TrayIconManager.cs b/src/RunnerV2/RunnerV2/Helpers/TrayIconManager.cs
index d30ed57f4d..85e750f45f 100644
--- a/src/RunnerV2/RunnerV2/Helpers/TrayIconManager.cs
+++ b/src/RunnerV2/RunnerV2/Helpers/TrayIconManager.cs
@@ -17,6 +17,8 @@ namespace RunnerV2.Helpers
 {
     internal static partial class TrayIconManager
     {
+        private static bool _trayIconVisible;
+
         private static nint GetTrayIcon()
         {
             if (SettingsUtils.Default.GetSettings<GeneralSettings>().ShowThemeAdaptiveTrayIcon)
@@ -31,19 +33,31 @@ namespace RunnerV2.Helpers
 
         public static void UpdateTrayIcon()
         {
+            if (!_trayIconVisible)
+            {
+                return;
+            }
+
             NOTIFYICONDATA notifyicondata = new()
             {
                 CbSize = (uint)Marshal.SizeOf<NOTIFYICONDATA>(),
                 HWnd = Runner.RunnerHwnd,
                 UId = 1,
                 HIcon = GetTrayIcon(),
-                UFlags = 0x0000001 | 0x0000002,
+                UFlags = 0x0000001 | 0x00000002 | 0x4,
+                UCallbackMessage = (uint)WindowMessages.ICON_NOTIFY,
+                SzTip = "PowerToys Runner",
             };
             Shell_NotifyIcon(0x1, ref notifyicondata);
         }
 
         internal static void StartTrayIcon()
         {
+            if (_trayIconVisible)
+            {
+                return;
+            }
+
             NOTIFYICONDATA notifyicondata = new()
             {
                 CbSize = (uint)Marshal.SizeOf<NOTIFYICONDATA>(),
@@ -57,16 +71,17 @@ namespace RunnerV2.Helpers
 
             ChangeWindowMessageFilterEx(Runner.RunnerHwnd, 0x0111, 0x0001, IntPtr.Zero);
 
-            new ThemeListener().ThemeChanged += (_) =>
-            {
-                PostMessageW(Runner.RunnerHwnd, 0x0800, IntPtr.Zero, 0x9000);
-            };
-
             Shell_NotifyIcon(NIMADD, ref notifyicondata);
+            _trayIconVisible = true;
         }
 
         internal static void StopTrayIcon()
         {
+            if (!_trayIconVisible)
+            {
+                return;
+            }
+
             NOTIFYICONDATA notifyicondata = new()
             {
                 CbSize = (uint)Marshal.SizeOf<NOTIFYICONDATA>(),
@@ -75,6 +90,7 @@ namespace RunnerV2.Helpers
             };
 
             Shell_NotifyIcon(NIMDELETE, ref notifyicondata);
+            _trayIconVisible = false;
         }
 
         internal enum TrayButton : uint
@@ -99,6 +115,10 @@ namespace RunnerV2.Helpers
             AppendMenuW(_trayIconMenu, 0u, new UIntPtr((uint)TrayButton.ReportBug), "Report a Bug");
             AppendMenuW(_trayIconMenu, 0x00000800u, UIntPtr.Zero, string.Empty); // separator
             AppendMenuW(_trayIconMenu, 0u, new UIntPtr((uint)TrayButton.Close), "Close");
+            new ThemeListener().ThemeChanged += (_) =>
+            {
+                PostMessageW(Runner.RunnerHwnd, 0x0800, IntPtr.Zero, 0x9000);
+            };
         }
 
         internal static void ProcessTrayIconMessage(long lParam)
diff --git a/src/RunnerV2/RunnerV2/Runner.cs b/src/RunnerV2/RunnerV2/Runner.cs
index 886d511706..29786cd264 100644
--- a/src/RunnerV2/RunnerV2/Runner.cs
+++ b/src/RunnerV2/RunnerV2/Runner.cs
@@ -81,7 +81,10 @@ namespace RunnerV2
             Logger.LogInfo("Runner started");
 
             InitializeTrayWindow();
-            TrayIconManager.StartTrayIcon();
+            if (SettingsUtils.Default.GetSettings<GeneralSettings>().ShowSysTrayIcon)
+            {
+                TrayIconManager.StartTrayIcon();
+            }
 
             if (SettingsUtils.Default.GetSettings<GeneralSettings>().EnableQuickAccess)
             {
@@ -295,7 +298,11 @@ namespace RunnerV2
                     TrayIconManager.ProcessTrayMenuCommand((nuint)wParam);
                     break;
                 case (uint)WindowMessages.WINDOWPOSCHANGING:
-                    TrayIconManager.StartTrayIcon();
+                    if (SettingsUtils.Default.GetSettings<GeneralSettings>().ShowSysTrayIcon)
+                    {
+                        TrayIconManager.StartTrayIcon();
+                    }
+
                     break;
                 case (uint)WindowMessages.DESTROY:
                     Close();
@@ -306,9 +313,31 @@ namespace RunnerV2
                         ToggleModuleStateBasedOnEnabledProperty(module);
                     }
 
+                    CentralizedKeyboardHookManager.RemoveAllHooksFromModule("QuickAccess");
+                    if (SettingsUtils.Default.GetSettings<GeneralSettings>().EnableQuickAccess)
+                    {
+                        CentralizedKeyboardHookManager.AddKeyboardHook("QuickAccess", SettingsUtils.Default.GetSettings<GeneralSettings>().QuickAccessShortcut, QuickAccessHelper.Show);
+                    }
+                    else
+                    {
+                        CentralizedKeyboardHookManager.RemoveAllHooksFromModule("QuickAccess");
+                        QuickAccessHelper.Stop();
+                    }
+
+                    TrayIconManager.UpdateTrayIcon();
+
+                    if (SettingsUtils.Default.GetSettings<GeneralSettings>().ShowSysTrayIcon)
+                    {
+                        TrayIconManager.StartTrayIcon();
+                    }
+                    else
+                    {
+                        TrayIconManager.StopTrayIcon();
+                    }
+
                     break;
                 default:
-                    if (msg == _taskbarCreatedMessage)
+                    if (msg == _taskbarCreatedMessage && SettingsUtils.Default.GetSettings<GeneralSettings>().ShowSysTrayIcon)
                     {
                         TrayIconManager.StartTrayIcon();
                     }