If you’re creating and sharing invoices in FreeAgent you will need to go to FreeAgent to mark an invoice as paid.
Mettle shares your transactions with FreeAgent when they have cleared, but we are not able to automatically match a payment to a FreeAgent invoice.
FreeAgent have a guide on marking invoices as paid here.
If you are having problems with FreeAgent Invoices you should contact FreeAgent support at email@example.com
If you’re using invoicing in the Mettle app and you’re unable to mark an invoice as paid contact us via in-app chat.