I'm glad you've reached out to us. Let me help and provide some options on how to mark the Invoice as paid in QuickBooks Online (QBO).
There are different options on how to close an open invoice, however, the process depends on the scenarios.
First, once an invoice becomes non-collectible, you'll need to write it off and declare it as a bad debt to clear the invoice out of your accounts receivable and reduce your net profit by its amount. You can check this article for the detailed steps on how to write off bad debt.
Second, if the invoice payment entered through Bank Deposit instead of Receive Payment, you'll need to link a deposit to an invoice so that it will mark as paid. For additional reference, you can check this article on how to link a deposit to an invoice.
Lastly, once an invoice got paid, you'll need to process Receive payment feature in QBO. For the detailed steps and video tutorial, please check this article: Receive Payments in QuickBooks.
You may also consult an accountant if you’re not familiar with the process and to ensure your books are accurate.
That's it! Please know that i'm just a post away if you have any other concerns about Invoice in QBO. Wishing you and your business continued success.