diff --git a/src/cli/global/update.rs b/src/cli/global/update.rs
index 7824091bb2..167b7c0b50 100644
--- a/src/cli/global/update.rs
+++ b/src/cli/global/update.rs
@@ -66,6 +66,9 @@ pub async fn execute(args: Args) -> miette::Result<()> {
             .expose_executables_from_environment(env_name)
             .await?;
 
+        // Sync shortcuts
+        state_changes |= project.sync_shortcuts(env_name).await?;
+
         Ok(state_changes)
     }
 
diff --git a/src/global/common.rs b/src/global/common.rs
index 29971fa96e..f8c7efd097 100644
--- a/src/global/common.rs
+++ b/src/global/common.rs
@@ -783,10 +783,10 @@ pub(crate) fn shortcut_sync_status(
             .swap_take(&record.repodata_record.package_record.name)
             .is_some()
         {
-            if !has_installed_system_menus {
-                // The package record isn't installed, but it is requested
-                records_to_install.push(record);
-            }
+            // Always install shortcut.
+            // Because pixi doesn't know if it is already installed,
+            // and still exists in system.
+            records_to_install.push(record);
         } else if has_installed_system_menus {
             // The package record is installed, but not requested
             records_to_uninstall.push(record);