Good to see you here, userkylie1.
You can create a Receive payment to manually mark the invoice as paid.
Here's how:
- Go to + New > Receive payment.
- Select the customer's name from the Customer drop-down list.
- Set the Payment date, Payment method, and Deposit to (You can use the Undeposited Funds account to deposit the money later on).
- Under the Outstanding Transactions, put a check mark on the invoice you want to pay.
- Click Save and close.
Please see this sample screenshot for a visual reference:
For more details, you can read this article: Record invoice payments in QuickBooks Online.
If you receive bank deposits from your customer, check out this link on how to record the payment: How to link a deposit to an invoice
I'll be right here if you have any follow-up questions about recording the payment or other concerns with your QuickBooks Online account, Have a great day!