Paid invoice

You would have to link it to the payment, for it to be showed as paid. 

Hi bodhiambo!

I agree with Just_me. There are various ways to pay an invoice, and I'm happy to share them with you.

If you received a payment physically and want to reflect it on the invoice, simply open the invoice, and click Receive payment. Then, enter the amount you received.

If the customer has an available credit note, overpayment, or prepayment recorded as a deposit, simply open the invoice and click Receive payment. Then, select those transactions in the Credits section, on the next page, to be applied as payment to the invoice.

You can also match a bank transaction (Deposit) to an invoice. This step will mark the invoice as paid.

If you're using our Merchant service, an invoice will automatically be marked as paid when a customer pays for it online.

Here's an article with a video tutorial for your additional reference: Record invoice payments in QuickBooks Online.

I'm just a comment away if you have other questions. Take care and enjoy your weekend!