This article is for small businesses that are not yet eligible for Making Tax Digital (MTD).
If you have signed up for MTD, go to Submit a VAT return to HMRC - MTD for small businesses.
From April 2019, all eligible UK VAT-registered businesses will have to keep their financial records in a digital form and submit their VAT returns using approved software. Find out whether you are eligible here.
If you are on the Flat Rate Scheme or submit your VAT annually and have not signed up for MTD, you will need to file through the HMRC Government Gateway. Once you have filed through the gateway, go to Mark your VAT as filed in QuickBooks to close the period.
You can now close the books to protect transactions entered in the quarter you just filed.
Once you have paid off the liability to HMRC, you can record a VAT payment or refund.