In QuickBooks Online, the best way to record your VAT payment is by going to the VAT section and recording the payment manually. You do not need to record this as an expense, as this payment clears a liability in your account.
Here's how:
Go to VAT, then select Overview.
From the Returns tab, find the return you've filed.
Select Record payment from the Action column.
Select the bank account you've used to pay HMRC.
Enter the Payment date and Payment amount in the appropriate fields.
You may add a Memo if needed, then select Save.
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