Refund outside of Quickbooks

Hello there, allenwolfe.

I'd be happy to help share additional insight about recording the payment and refund in QuickBooks Online. 

If a customer paid you more than what was owed, returning product, requesting a refund you can create a Credit Memo. Once done, you can apply it to an open invoice for a given customer. 

1. From the + New icon, choose Credit memo.
2. Enter the customer's name to be refunded.
3. In the Product/Service column, pick the item being refunded.
4. Add the correct amount you are going to refund the customer before clicking Save and close.

Let me share these articles for more details on how to record a refund or apply a credit memo: 

• Create and apply credit memos or delayed credits in QuickBooks Online.
• Record a customer refund in QuickBooks Online.

Please let me know if you have any other questions about recording the payment or refund, I’ll be glad to help. Have a nice day!

I understand the credit memo part for the one customer, but we didn't actually refund via bank account. The company website provider refunded the customer from other customer's payments that we were to get. So how do I show that those customers paid without actually receiving the payment on our end because their payments refunded the other customer through the website domain (Wix)?

It's great to see you here in the Community, @wencommunication.

I'm here to lend a hand in recording customer payments and refunds from website providers in QuickBooks Online (QBO).

You can record the payment as a journal entry and then link it to the invoice as paid. For this, you will need to create a clearing account (Cash on Hand) to hold funds so it doesn't affect your bank balance. See this:
 

Then you can receive the journal entry as payment towards the invoice. Choose the same bank as the holding account on the journal entry in the Deposit field. Here's how you do it:

Once done, you can create a reversal entry to offset the balance on the holding account. That way, there is no longer an A/R balance and your bank balance isn't affected by the transaction.

Before doing any of these steps, you seek an accountant's approval and guidance. This method may affect your financials and past reconciliations, so it needs a professional point of view.

I'll share this related article with you which has the overview of resolving customer balances and how to fix them: Resolve A/R or A/P balances on a cash basis Balance Sheet

If you have other concerns, please let me know in the comment below. I'll be right here if you need further assistance with recording the payment. Have a nice day!