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Good day, @hareintheforest.
Let me share information on how to apply the unapplied payments in QuickBooks Desktop.
The unapplied payments happen if invoices have been deleted, customer's overpaid, or they aren't applied to an invoice.
In your case, you may have received invoice payments directly without applying for the unapplied payment. To resolve this, you can delete the payment link to the invoice and apply for the payment.
To delete the payment, here's how:
Once done, to apply for the unapplied payment, follow the below steps:
For future help, I'm attaching an article below that will give you the answers you need for QuickBooks Desktop: Get QuickBooks Desktop user guides.
That's it. If you have any follow up questions or clarifications this process, please leave a comment below. Have a great day.