Do you have to set up a direct debit to pay VAT or can you manually pay it online?

Hello, @henribrandman.

Currently, paying VAT through QuickBooks is not available 

 You can record your VAT payments and file your VAT returns in QuickBooks.  However you would physically need to pay it directly through to HMRC via the usual methods. Here's how to record a VAT payment in Quickbooks.*Go to Taxes and click on Record Payment for the specific VAT period you need.*At the top, select the bank account you've used to pay HMRC.*Make sure you've selected Payment under Payment Type.*Enter the payment date and amount*.Add a memo if needed.*Click Save

You can refer to this article for more detailed instructions about recoding VAT payments: How to record a VAT payment.

Let me know if you have other questions about VAT in QuickBooks. I'm always here to help.