If a customer pays my invoice online with their checking account, can I refund it online or do I have to issue a manual check?

Hello there, paigeh.

When your customer pays the invoice with their checking account, we can search using the existing Check Transaction in the Merchant Service Center. It's how we can refund online. Here's how:

1. Sign in on the Merchant Service Center Portal.
2. From the Processing Tools section, select Void an eCheck.
3. Select the appropriate eCheck to void.
4. Click Submit.

Note: Once a transaction is not available, this can no longer be voided.

If you want to record the customer's refund in QBO, you can record it using an expense or check. Please check this article for the complete steps: Record a customer refund in QuickBooks Online. 

Lastly, I'm adding an article where you can view the outlines about voiding a check transaction within Merchant Service Center.

Please comment below if you have other questions or need more help with QuickBooks. Have a good one!

Hi paigeh,

Hope you’re doing great. I wanted to see how everything is going about processing refund your customer through online. Was it resolved? Do you need any additional help or clarification? If you do, just let me know. I’d be happy to help you at anytime.

Looking forward to your reply. Have a pleasant day ahead!