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Incorporation fee - VAT problem

When we were incorporated, our account did the paperwork and invoiced us with VAT included. It is now end of year time and they have now told us 12 months later that HMRC do not allow us to claim back the VAT on that - which we did do 9 months ago.

Our accountant has said it can be cleared up with a credit note. This is fine in theory, but I can't figure out how to do in in FA. I can create a credit note to cancel out the original invoice fine, but how do reinput it as gross with no VAT as a bill - there will be no actual payment therefore adding a manual bank account entry will not tally with our actual bank statement????

Confused.....

How should I have added the invoice in the first place to FA?
 
sad I’m confused
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