Why does my invoice to my customer say unpaid, but my customer has proof showing he’s paid the invoice?

How did your customer pay?   did they pay using qbo payments?  Did they pay by check?  Did you enter the payment and clear the invoice?

Lynda

Let's perform some troubleshooting solutions to mark the invoice as paid, christopher-k-sh.

We can review the applied payment to all the invoices in QuickBooks Online (QBO). Let;s make usre the Receive Payment transaction is linked the correct one. If not, we can delete it and apply the payment to the right invoice.

Here's how:

1. Click Sales from the left menu.
2. Choose Invoices, and click the invoice to open it. 
3. Under Payment Status, click the 1 payment link and click on the Date hyperlink.
4. Click the More tab and choose Delete.
5. Click Yes to confirm.

Then, enter the payment again to the correct invoice. Just follow the steps and details in this article: Record an invoice payment.

If the invoice payment is entered through Bank Deposit instead of Receive Payment, we need to link them to an invoice. Doing this will mark the transaction as paid.

You can refer to How to link a deposit to an invoice article for the detailed steps.

I've got a link here that provides you with articles about managing customer payments: Manage payments. 

That's it! Please know that I'm just a post away if you need a hand with creating recurring transactions or any QBO related. Wishing you and your business continued success.