When you run a Customer Refund and credit the money back to their credit card, it’s possible that your refunds were higher than your sales that day. Sometimes your merchant services daily batch total is negative. But currently there’s no way to create negative deposits in QuickBooks Online. Here is the workaround.
To clear the Refund out of Undeposited Funds, create a Journal Entry debiting Undeposited Funds and crediting the bank account. When you go to the Bank Deposit window, the negative and positive Refund will cancel each other out. The negative will still show in the bank register.
Group & deposit all the credit sales for the day as you would normally.
When you reconcile at the end of the month, don’t forget that you had a day when your QuickBooks checking register won’t match your bank statement. When you reconcile, you’ll need to mark off the deposit and the offsetting withdrawal manually. Your totals for the Deposits and Expenses columns won’t match the bank statement. There’s nothing you can do but eyeball it.
Hopefully you won’t have many days where you refund more than you made that day in credit card sales, but when you do, now you’ll know how to get rid of that pesky negative sale.