Can a CIS return be marked as submitted?

Yes, you can absolutely do that. Since your accountant used their own software, you can use the Mark as Filed feature in QuickBooks. This clears those old periods off your dashboard without sending any duplicate data to HMRC, giving you a totally clean slate to start sending your own returns this year.

Here's how:

1. Head over to All apps, then Payroll, and select Payroll taxes.
2. Click on CIS, find the period that your accountant has already submitted, and then hit File return.
3. Double-check that the details are correct, read the declaration, and tick the box to agree.
4. Click the small dropdown arrow right next to the Submit to HMRC button and select Mark as Filed.

You can also refer to this article for more details about the process and what to do before you start filing your own returns: File a CIS return in QuickBooks.

Feel free to add a reply below if you have other concerns.