diff --git a/Flow.Launcher/App.xaml.cs b/Flow.Launcher/App.xaml.cs
index 87677f58a..87698a545 100644
--- a/Flow.Launcher/App.xaml.cs
+++ b/Flow.Launcher/App.xaml.cs
@@ -202,18 +202,11 @@ namespace Flow.Launcher
         {
             // we try to enable auto-startup on first launch, or reenable if it was removed
             // but the user still has the setting set
-            if (_settings.StartFlowLauncherOnSystemStartup && !Helper.AutoStartup.IsEnabled)
+            if (_settings.StartFlowLauncherOnSystemStartup)
             {
                 try
                 {
-                    if (_settings.UseLogonTaskForStartup)
-                    {
-                        Helper.AutoStartup.EnableViaLogonTask();
-                    }
-                    else
-                    {
-                        Helper.AutoStartup.EnableViaRegistry();
-                    }
+                    Helper.AutoStartup.CheckIsEnabled(_settings.UseLogonTaskForStartup);
                 }
                 catch (Exception e)
                 {
diff --git a/Flow.Launcher/Helper/AutoStartup.cs b/Flow.Launcher/Helper/AutoStartup.cs
index 81568875e..b83bb5948 100644
--- a/Flow.Launcher/Helper/AutoStartup.cs
+++ b/Flow.Launcher/Helper/AutoStartup.cs
@@ -16,29 +16,37 @@ public class AutoStartup
     private const string LogonTaskName = $"{Constant.FlowLauncher} Startup";
     private const string LogonTaskDesc = $"{Constant.FlowLauncher} Auto Startup";
 
-    public static bool IsEnabled
+    public static void CheckIsEnabled(bool useLogonTaskForStartup)
     {
-        get
+        // We need to check both because if both of them are enabled,
+        // Hide Flow Launcher on startup will not work since the later one will trigger main window show event
+        var logonTaskEnabled = CheckLogonTask();
+        var registryEnabled = CheckRegistry();
+        if (useLogonTaskForStartup)
         {
-            // Check if logon task is enabled
-            if (CheckLogonTask())
+            // Enable logon task
+            if (!logonTaskEnabled)
             {
-                return true;
+                Enable(true);
             }
-
-            // Check if registry is enabled
-            try
+            // Disable registry
+            if (registryEnabled)
             {
-                using var key = Registry.CurrentUser.OpenSubKey(StartupPath, true);
-                var path = key?.GetValue(Constant.FlowLauncher) as string;
-                return path == Constant.ExecutablePath;
+                Disable(false);
             }
-            catch (Exception e)
+        }
+        else
+        {
+            // Enable registry
+            if (!registryEnabled)
             {
-                App.API.LogError(ClassName, $"Ignoring non-critical registry error (querying if enabled): {e}");
+                Enable(false);
+            }
+            // Disable logon task
+            if (logonTaskEnabled)
+            {
+                Disable(true);
             }
-
-            return false;
         }
     }
 
@@ -69,22 +77,28 @@ public class AutoStartup
         return false;
     }
 
+    private static bool CheckRegistry()
+    {
+        try
+        {
+            using var key = Registry.CurrentUser.OpenSubKey(StartupPath, true);
+            var path = key?.GetValue(Constant.FlowLauncher) as string;
+            return path == Constant.ExecutablePath;
+        }
+        catch (Exception e)
+        {
+            App.API.LogError(ClassName, $"Ignoring non-critical registry error (querying if enabled): {e}");
+        }
+
+        return false;
+    }
+
     public static void DisableViaLogonTaskAndRegistry()
     {
         Disable(true);
         Disable(false);
     }
 
-    public static void EnableViaLogonTask()
-    {
-        Enable(true);
-    }
-
-    public static void EnableViaRegistry()
-    {
-        Enable(false);
-    }
-
     public static void ChangeToViaLogonTask()
     {
         Disable(false);
diff --git a/Flow.Launcher/SettingPages/ViewModels/SettingsPaneGeneralViewModel.cs b/Flow.Launcher/SettingPages/ViewModels/SettingsPaneGeneralViewModel.cs
index 021c9d7fe..6b56caf5e 100644
--- a/Flow.Launcher/SettingPages/ViewModels/SettingsPaneGeneralViewModel.cs
+++ b/Flow.Launcher/SettingPages/ViewModels/SettingsPaneGeneralViewModel.cs
@@ -48,11 +48,11 @@ public partial class SettingsPaneGeneralViewModel : BaseModel
                 {
                     if (UseLogonTaskForStartup)
                     {
-                        AutoStartup.EnableViaLogonTask();
+                        AutoStartup.ChangeToViaLogonTask();
                     }
                     else
                     {
-                        AutoStartup.EnableViaRegistry();
+                        AutoStartup.ChangeToViaRegistry();
                     }
                 }
                 else