Clients who set up auto pay on recurring invoices are being charged full original total and credits are not being considered

It’s great to see you participating in the Community forum, Kfryzelwolff. Let us help you fix the auto-pay issues with recurring invoices that are not applying credits in QuickBooks.

QuickBooks auto-pay feature currently charges the original invoice amount rather than the adjusted amount that includes applied credits. To address this, please ask your clients who have set up auto-pay to temporarily disable the feature.

Explain to your clients that credits cannot be processed automatically under the auto-pay system. Disabling auto-pay will help prevent further overpayments while ensuring that credits are appropriately applied.

Next, manually send payment links to the affected clients for future invoices. This will ensure that credits and adjustments are reflected in the amount they owe.

For any existing overpayments, you can either issue a refund or apply the overpayment as a credit toward future invoices. For more details about the process, see the article: Handle a customer credit or overpayment in QuickBooks Online.

Please let us know if you have any follow-up questions. We’re here to help in any way we can.

Hello there, Kfryzelwolff.

I just wanted to follow up to check if the resolution we provided helped resolve your issue. Please let us know if everything is now working as expected or if you’re still experiencing any problems.
 
We’ll be glad to assist further if needed.