Hello there, @accounting95,
Thank you for joining QuickBooks Community! Let’s match the payment so you can get rid of the negative open balance.
Once you overpay a bill, QBO will automatically save the overpayment as an unapplied credit that you can add to the next payment.
To fix this, I recommend you delete the second invoice and its recorded payment. Then create a new bill for the total amount of service/item, but do not deduct the overpayment.
Once done, you can pay the second bill and apply the credit to zero out the vendor balance.
Here are the steps:
1. Select the Plus icon (+), then click Expense.
2. In the Choose a payee drop-down, select the vendor name.
3. Select the second bill, then click Make Payment.
4. From the Add to Expense column, select Add for the outstanding vendor credit. If it has been added, make sure both the bill and unapplied payment are checked.
5. Click Save and Close.
Give this a try and let me know how it goes by posting a comment below. We are always here to help should you have follow-up questions. Have a great day ahead!
"To fix this, I recommend you delete the second invoice and its recorded payment. Then create a new bill for the total amount of service/item, but do not deduct the overpayment."
Payment need not be deleted, just unapplied to new net bill unless the payment was recorded as an expense without a bill. Enter or edit new bill from vendor for total before application of overpayment as this represents full purchase. Then you can apply both the short payment and the existing credit to the new bill ending in zero balance.