Hello.Is there a way I can send an invoice through quickbooks, then for it to mark as paid when paid through bank transfer?

Hi Joe,

Welcome to the community!

There is currently no option to do this, however if you have a bank feed connected the payment will offer a match to the invoice which will then mark the invoice as paid.

when you get paid, use receive payments against that invoice, then deposit the payment

download banking if you use it and match