Yes, mandagh73. Your invoice will be marked as paid after you receive the payment.
There are a few different ways to mark an invoice as paid. You can go to the Sales tab and select Invoices or create a Receive Payment to mark it as paid in QuickBooks. Let me show you how:
- On the left navigational bar, go to the Sales tab.
- Select Invoices.
- Choose the invoice, and then from the Action column, click the Receive payment button.

For the received payment:
- Click + New, then select Receive payment.
- From the Customer drop-down, select the name of the customer.
- From the Payment method drop-down, select the payment method.
- From the Deposit to drop-down, select the account you put the payment into.
- From the Outstanding Transactions section, mark all open invoices of the customer.
- Click Save and close.


For more information, check this article: Record invoice payments in QuickBooks Online. Once done go to the All Sales tab to verify the invoices that are paid.
On top of that, I'll be adding these resources that will guide you in personalising your sales forms and ensuring payments will be deposited to the correct accounts in QuickBooks:
Don't hesitate to leave a comment below if you have any questions. I'm here to help.