How to file annual return for my own ltd to hmrc via quickbooks?

Can you confirm which annual return you mean? This term is often used loosely and could refer to one of two different things, either Confirmation Statement or Corporation Tax Return (CT600).

If it is for the Confirmation Statement, QuickBooks does not handle this, so you (or your accountant) must submit it via the Companies House portal.

While standard QuickBooks can't file a CT600 return by itself. To file through QuickBooks, you must work with an accountant using QuickBooks Online Accountant via Workpapers. For more guidance, check this article: File your Corporation Tax return using Workpapers in Intuit Accountant Suite. 

Before proceeding, ensure your books are fully reconciled for the financial year to guarantee accurate figures.

Let us know below if you have any questions. We’re here to help.