diff --git a/src/runner/settings_window.cpp b/src/runner/settings_window.cpp
index 473fa7ebe3..e31b934d40 100644
--- a/src/runner/settings_window.cpp
+++ b/src/runner/settings_window.cpp
@@ -148,16 +148,19 @@ std::optional<std::wstring> dispatch_json_action_to_module(const json::JsonObjec
     return result;
 }
 
-void send_json_config_to_module(const std::wstring& module_key, const std::wstring& settings)
+void send_json_config_to_module(const std::wstring& module_key, const std::wstring& settings, bool hotkeyUpdated)
 {
     auto moduleIt = modules().find(module_key);
     if (moduleIt != modules().end())
     {
         moduleIt->second->set_config(settings.c_str());
 
-        moduleIt->second.remove_hotkey_records();
-        moduleIt->second.update_hotkeys();
-        moduleIt->second.UpdateHotkeyEx();
+        if (hotkeyUpdated)
+        {
+            moduleIt->second.remove_hotkey_records();
+            moduleIt->second.update_hotkeys();
+            moduleIt->second.UpdateHotkeyEx();
+        }
     }
 }
 
@@ -166,7 +169,22 @@ void dispatch_json_config_to_modules(const json::JsonObject& powertoys_configs)
     for (const auto& powertoy_element : powertoys_configs)
     {
         const auto element = powertoy_element.Value().Stringify();
-        send_json_config_to_module(powertoy_element.Key().c_str(), element.c_str());
+
+        /* As PowerToys Run hotkeys are not registered by the runner, hotkey updates are
+         * triggered only when hotkey properties change to avoid incorrect conflict detection; 
+         * otherwise, the existing logic remains.
+         */
+        auto settings = powertoy_element.Value().GetObjectW();
+        bool hotkeyUpdated = true;
+        if (settings.HasKey(L"properties"))
+        {
+            const auto properties = settings.GetNamedObject(L"properties");
+
+            // Currently, only PowerToys Run settings use the 'hotkey_changed' property.
+            json::get(properties, L"hotkey_changed", hotkeyUpdated, true);
+        }
+        
+        send_json_config_to_module(powertoy_element.Key().c_str(), element.c_str(), hotkeyUpdated);
     }
 };
 
diff --git a/src/settings-ui/Settings.UI.Library/PowerLauncherProperties.cs b/src/settings-ui/Settings.UI.Library/PowerLauncherProperties.cs
index 590fb2e290..08eb16a389 100644
--- a/src/settings-ui/Settings.UI.Library/PowerLauncherProperties.cs
+++ b/src/settings-ui/Settings.UI.Library/PowerLauncherProperties.cs
@@ -94,6 +94,9 @@ namespace Microsoft.PowerToys.Settings.UI.Library
         [JsonPropertyName("generate_thumbnails_from_files")]
         public bool GenerateThumbnailsFromFiles { get; set; }
 
+        [JsonPropertyName("hotkey_changed")]
+        public bool HotkeyChanged { get; set; } = false;
+
         [CmdConfigureIgnoreAttribute]
         public HotkeySettings DefaultOpenPowerLauncher => new HotkeySettings(false, false, true, false, 32);
 
diff --git a/src/settings-ui/Settings.UI/ViewModels/PowerLauncherViewModel.cs b/src/settings-ui/Settings.UI/ViewModels/PowerLauncherViewModel.cs
index 31efe28260..ee5b6e2f7c 100644
--- a/src/settings-ui/Settings.UI/ViewModels/PowerLauncherViewModel.cs
+++ b/src/settings-ui/Settings.UI/ViewModels/PowerLauncherViewModel.cs
@@ -31,6 +31,7 @@ namespace Microsoft.PowerToys.Settings.UI.ViewModels
         private bool _enabledStateIsGPOConfigured;
         private bool _isEnabled;
         private string _searchText;
+        private bool _hotkeyChanged;
 
         private GeneralSettings GeneralSettingsConfig { get; set; }
 
@@ -162,6 +163,12 @@ namespace Microsoft.PowerToys.Settings.UI.ViewModels
             // Notify UI of property change
             OnPropertyChanged(propertyName);
 
+            // Since PowerLauncher registers its hotkeys independently within the module process,
+            // the runner is notified to update PowerLauncher’s hotkeys only when changes occur.
+            // This prevents incorrect conflict detection results.
+            settings.Properties.HotkeyChanged = _hotkeyChanged;
+            _hotkeyChanged = false;
+
             callback(settings);
         }
 
@@ -335,6 +342,7 @@ namespace Microsoft.PowerToys.Settings.UI.ViewModels
                 if (settings.Properties.OpenPowerLauncher != value)
                 {
                     settings.Properties.OpenPowerLauncher = value ?? settings.Properties.DefaultOpenPowerLauncher;
+                    _hotkeyChanged = true;
                     UpdateSettings();
                 }
             }
diff --git a/src/settings-ui/Settings.UI/ViewModels/ShortcutConflictViewModel.cs b/src/settings-ui/Settings.UI/ViewModels/ShortcutConflictViewModel.cs
index 6c6d624f97..48d1d09a40 100644
--- a/src/settings-ui/Settings.UI/ViewModels/ShortcutConflictViewModel.cs
+++ b/src/settings-ui/Settings.UI/ViewModels/ShortcutConflictViewModel.cs
@@ -242,6 +242,15 @@ namespace Microsoft.PowerToys.Settings.UI.ViewModels
                     // No need to save settings here, the runner will call module interface to save it
                     // SaveSettingsToFile(settings);
 
+                    // For PowerToys Run, we should set the 'HotkeyChanged' property here to avoid issue #41468
+                    if (string.Equals(moduleName, PowerLauncherSettings.ModuleName, StringComparison.OrdinalIgnoreCase))
+                    {
+                        if (settings is PowerLauncherSettings powerLauncherSettings)
+                        {
+                            powerLauncherSettings.Properties.HotkeyChanged = true;
+                        }
+                    }
+
                     // Send IPC notification using the same format as other ViewModels
                     SendConfigMSG(settingsConfig, moduleName);
                 }