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Recording this in QuickBooks will depend on whether you receive the VAT invoice or not, Lynne.
If the invoice is yet to be received, simply record it as a payment/cheque to a supplier, Category = Accounts Payable or Creditors & NO VAT. The deposit should now reflect as a credit amount against the supplier.
Here's how:
However, if you have received the invoice, enter it before putting the final payment and use the credit amount.
Alternatively, you can enter a dummy invoice from the supplier, then place the payment as you would a normal bill payment. Once you have the actual one, modify the dummy as required.
On top of that, I recommend contacting your accountant to further guide you in this process since this involves recording money movement transactions that might affect your book balance.
Leave a comment below if you need additional assistance recording your VAT transactions.