If you've issued an invoice in a foreign currency, your customer should of course pay you for that!
But at the moment, you'll need to enter that receipt into FreeAgent in your business's main currency, so £ sterling for our UK users. At the moment FreeAgent can't support multi-currency banking.
So how do you enter the money in £ sterling?
If you're explaining your bank transactions from an upload, you'll see the receipt come in in £ sterling.
When you explain that invoice receipt, if you choose an invoice that was in a foreign currency, FreeAgent gives you another value box here.

In this box, you need to put what the equivalent value in the foreign currency was.
So if your customer has paid you in full for the invoice, just put in the same amount as you issued the invoice for. FreeAgent will fill this in automatically.
If your customer has paid you in part, then you'd need to check with your customer how much he/she was paying you in the foreign currency, and overtype FreeAgent's figure. Your customer would need to tell you, for example, "I'm paying you €100".
If your customer is paying you net of any charges or commission, then you'd need to split the sterling amount, but don't adjust the foreign currency amount. This is so that FreeAgent will mark the right amount of the invoice as paid.
A realized currency gain or loss crystallizes on this invoice once it's fully or partly paid.
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