Should you be late filing your VAT Return or any other return to HMRC you run the risk of a late payment charge or possibly interest on the amount.

These would be processed as a journal entry, if you don't have a code for this you can create a new one within your chart of accounts, making sure the vat option states Without VAT as the amount charged should not appear on your vat return.

Currently, late payment charges are VAT exempt, so if you impose a late payment charge or interest onto a customer who has not paid then you do not add VAT to this amount on your invoice.