There is another option:

If you already have processed a pre-payment/over-payment, the result will be a credit on the customer's account.

If you check the box for Preferences > Business > Invoices > 'Process payments on posting', then when you post the next invoice for that customer, GnuCash will automatically apply that credit.

If you then choose the option for the Invoice Report to 'show payments' you'll see the credit applied.

This saves you a few steps, but both methods work.

Regards,
Adrien

On 6/3/22 8:40 AM, Ryan Carver wrote:
I just stumbled through this issue as well.  I was able to get a $2,000
customer credit to show as a payment on a new invoice by doing the
following steps:

1) create new invoice and post to A/R.
2) select new invoice and make payment.
3) when the payment window opens select the outstanding credit plus the
new invoice amount.
4) in the payment amount section enter $0.00.  This should apply the
credit to the new invoice.
5) print new invoice.  When printing new invoice select the Options tab
then Diplay tab and make sure "payments" are selected to print.
6) print new invoice as PDF and verify the customer credit was applied

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