MTD ITSA: does Quickfile report the NET income (i.e. after deducting the VAT) when generating quarterly updates? If not, is there a facility to deduct the VAT before submitting the update? Otherwise, how can you show payments made to HMRC on each VAT return throughout the year; they are not included in expenses?
All the reporting in QuickFile is the net numbers - the VAT never belongs to you in the first place and only exists on your balance sheet, not your P&L. Sales and purchase invoices put the VAT element into the relevant sales or purchase tax control account, the VAT return journal moves it from there to “VAT liability”, and the payment to (or refund from) HMRC offsets the liability account.