Refunding only part of a credit card transaction through QB Payments

Let me help you check if you can enter a partial refund, Maverick2.

In the Issue a Refund window, you can click the Refund amount field to check if you can enter a partial amount. If the system allows you to modify and enter a different amount, then follow step #7.

A credit memo will then appear on the customer's profile on your QuickBooks Desktop file.

If you aren't able to enter a partial amount, click Cancel to close the window. Then, process a refund outside of your QuickBooks company file. Here's how:

1. Sign in to your QuickBooks Payments account.
2. From the Processing Tools drop-down, select Reverse a Transaction.
3. Fill out the necessary fields and select Search.
4. Select the transaction you want to refund.
5. Manually type in the amount you want to refund in the Amount field, then Submit.
6. A new message will appear. You'll be asked to select Continue to process a full refund. If you'd like to submit a different amount, select Cancel. You'll then be prompted to enter a different refund amount. Select Continue.
7. A receipt of the transaction will display on the screen. 
8. Select E-mail or Print to get a copy of the receipt.

You can browse this article as a reference to the steps above: Void or refund transactions in QuickBooks Payments.

If you need more assistance about the process, I recommend contacting our QuickBooks Payments Team. They can guide you through the process in a secure environment.

For the credit memo, you have the option to apply it to future invoices. Check out this article for the process: Give your customer a credit or refund in QuickBooks Desktop for Windows.

Stay in touch with me if you have follow-up questions. Just leave a comment below and Ill get back to you.

Thank you for that information. However, what is the answer to question #2 in the original post:

1. Because I did the refund in Merchant Service Center, will the credit that comes back automatically match up with the credit memo?

Here's what is pending in my system. Will that -44.13 apply to the credit memo and zero out the customer's balance? Right now he has a -44.13 balance. See screenshot. Where does this go when it is recorded?

Thank you for your help, I appreciate it.

It's good to know that my colleague was able to provide the information you need and resolve your issue.

Please let us know if you still have questions. You're always welcome to post here in QuickBooks Community. Take care and have a good one.

@Kurt_M 

Unfortunately this did not work as you had explained it would. I will include some sample numbers here to tell you what happened (different numbers than in the screeshot so ignore those).

1. Invoice was for $100. I wanted to refund $10.
2. I created the credit memo for $10. Customer account is now at -$10.
3. I went to merchant service center and did the refund in there for $10.
4. The $10 credit showed up in the "Record Merchant Service Deposits" but I did not do anything, I was going to wait for it to automatically apply. (Auto apply setting is ON).
5. When the $10 went through, I could not find it anywhere. It did not go into my CC Clearing account.
6. To make matters more complicated, I had a receipt that went through on the same day for $200. The deposit into my actual bank account was $150 ($200 - $50). The deposit recorded into the QB register was $200 though. Now I had a $50 positive balance in my CC Clearing account in QB. This was $50 too much.
7. To fix the CC Clearing balance, I just did an adjustment.

The customer record still showed a -$10 balance. To get rid of that I just deleted the credit memo. 

This does not seem like it works correctly. Where did that $10 credit go? I didn't get recorded anywhere in QB. Seems very complicated and incorrect to me.