The customer made a partial payment on an invoice online with a credit card. When I sent the customer the invoice after applying the partial payment it says the invoice was paid already and will not allow him to pay the balance.
Good to see you here in the QuickBooks Community, @HHAvocado.
Let me help guide you about recording a partial payment from customer in QuickBooks Desktop.
In cases like this, you can delete the customer's payment from online and manually received the payment in QuickBooks to record the amount as partial payment for an invoice.
To record a partial payment, here's how:
For additional reference, you can check this article: Record a payment for an invoice.
That should do it! Don't hesitate to leave a comment below if you have additional questions about the invoice payment. I'll be happy to answer them for you. Wishing you and your business continued success.