If you have credit balance in customer’s account (A/R) and need to refund customer by payment (by check or by online), you should be using Check or Expense under Vendors header, not Refund Receipt form which works differently.

From home page screen, click “+1” sign
Select check (or expense if you paying online) under Vendors header
Select Customer from drop-down that need refund
Go to Account under Account details = Accounts Receivable (A/R)
Amount = refund amount
Save and Close
This entry will clear customer balance due account.

Note: If you have already used Refund Receipt form for this customer, need to delete that entry. That entry all it does is, takes out money from the bank account and also will reduce the income (or selected account for product/service). It does nothing with Customer account/Accounts Receivable account.

SECOND NOTE:

When to use Refund Receipt under Customers header?

If you have originally created Sales Receipt, to invoice your customer and payment received at the time of sale, and now you need to refund money to your customer that is only time use “Refund Receipt” form.

When to use Credit Memo under Customers header?

You have originally created Invoice and received payment and account has zero balance. And, you need to refund money (for whatever reason over-billing / returned item), you will need to create Credit Memo first. And, then issue refund money, using either check (or expense) form under Vendors header.