Here's how to record a receipt from your customer that pays off just one invoice. (You can also mark more than one invoice as paid with one payment.)
If you're uploading your bank transactions, you'll see the receipt coming in as one of your unexplained transactions.
Click on the receipt.

Then explain it with type Invoice Receipt, and choose the invoice your customer paid you for, from the drop-down menu.

Save that explanation.
When you've marked an invoice as sent, you'll see it has a button at the top saying "Add a Manual Payment".

If the money was paid into your primary bank account in FreeAgent, you can use this button to mark the invoice as paid. If the money was paid into a different account (for example, your business's savings account, or your cash account), don't use this button.
To use the Add a Manual Payment option, just click the button.
Fill in the details on this screen, including when the invoice was paid.

Save that entry.
You can use this option even if you're explaining uploaded transactions. When you explain this receipt, you'll see an extra box asking if you want to use an existing manual entry. Click the Use Selected Entry button.

If you're not uploading your bank transactions for the bank account which this receipt arrived in, and that bank account isn't your primary bank account, then you'll need to enter a manual invoice receipt.
Use type Invoice Receipt and choose the invoice from the drop-down list of invoices, like this.

Save the entry.
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