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Assigning multiple invoices to a single bank transaction.

I have a rather odd situation which I need some guidance on.

We have a subscription model for charging our clients which is collected by a payment provider. So for example we would create two invoices of £70 each which we would send to the client.

The payment provider would collect the £70 from each client and take £1.25 from each payment, they would also charge VAT on the £1.25.

So we have £140.00 - £2.50 - £0.38 = £137.12

When we do our bank upload we can only assign one invoice to the payment and we are not sure how to handle the missing £2.88 from the invoices?

Some advice would be great.
 
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