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This case seems unusual since this will leave an outstanding customer balance. In your case, I suggest receiving the payment normally.
Here's how:
Then you can write off the outstanding balance for invoices by following this article: Write off bad debt in QuickBooks Online.
By performing this method, your customer won't have an outstanding balance, and at the same time, the transactions will reflect properly. If you seem confused about what books to choose to account for the amounts, I recommend consulting your accountant for professional advice.
Additionally, here are a few things you can check if you'd like to give a credit to your customers: Create and apply credit memos or delayed credits in QuickBooks Online.
Please don't hesitate to comment if you have other questions. I'm always here to help you more. Keep safe.