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Incorrect VAT calculated for payment to initial debtor?

We operate VAT on a cash basis, and are having problems with the VAT calculations for some invoices which have been recorded as payments to initial debtors.

In one case we have a payment for £881.25 for an invoice which was issued before the VAT rate changed to 15%. This should be £750 plus VAT at 17.5% (£131.25), but Freeagent is calculating the VAT paypable as £114.95 (which is 15%).

I can't see a way of specifying a custom VAT rate for payments to initial debtors like you can for invoice payments, is there some way I can work around this?
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