How to Refund a Payment (Full or Partial)

This article walks through refunding a payment in Biller Genie. You can issue full refunds or partial refunds on Credit Card, Stored Card, and ACH transactions, and the refund automatically syncs back to your accounting software — as a refund receipt in QuickBooks Online, or as a credit memo against the customer plus a check that funds the credit memo (the standard QuickBooks Desktop way of recording a refund) in QuickBooks Desktop (via MagicCarpet).

Before you start

Refunds are available after a transaction has settled. If the transaction is same-day for Credit Card, or hasn't yet been submitted to the Federal Reserve for ACH, you might be able to void it instead — voids are instant and don't incur fees. See Voids vs Refunds: When to Use Each for the full timing breakdown.

Issuing a refund

1. In the Merchant Portal, open the transaction you want to refund.
2. Click the Refund button.
3. The refund modal opens, defaulted to a full refund. If you want a partial refund instead, toggle to Partial and enter the amount.
4. For partial refunds, choose how technology fees should be handled:
   • Inclusive — the customer gets the full transaction amount back (you absorb the technology fee).
   • Exclusive — the customer gets the principal back; the technology fee stays.
5. Review and confirm.

The customer will see the credit return to their original payment method in 3 to 5 business days.

Multiple partial refunds

You can issue multiple partial refunds against the same transaction. The cumulative refund amount can total up to the original payment amount. Once cumulative refunds equal the original payment, the transaction is fully refunded and no further refunds are possible on it.

Bulk refunds

If a customer paid multiple invoices in one bulk transaction, you can refund some or all of that bulk payment in a single action. See Bulk Refunds and Bulk Voids for the bulk walkthrough.

What happens in your accounting software

When the refund completes, Biller Genie creates a matching record in your accounting software:

QuickBooks Online

• A refund receipt is created in QuickBooks Online.
• The refund is split back into the original line items, with each amount credited back to the account it originally came from (proper GAAP accounting).
• Refunded tax amounts flow back to the original tax authority.
• The Biller Genie transaction ID is written into the description field for cross-reference.
• For full refunds against an invoice, the original invoice reopens.

QuickBooks Desktop (via MagicCarpet)

• A credit memo is created and applied to the original invoice. (QuickBooks Desktop doesn't have a refund-receipt concept, so the credit memo serves the same role.)
• Line items and tax follow the same GAAP-correct split as QuickBooks Online.
• The Biller Genie transaction ID is written into the description.
• Voids delete the corresponding payment in QuickBooks Desktop (which does not support voiding payment records) and reopen any associated invoices.

The Chart of Accounts: Mapping Your Accounts in Biller Genie mapping tool controls which accounts Biller Genie writes to. If your mapping is set up correctly, the refund just appears in the right places — no manual reconciliation needed.

FAQs

How do I process a refund?

Open the transaction in your Merchant Portal, click Refund, choose full or partial, set technology-fee handling, confirm. That's it.

Can I refund just part of a credit card transaction?

Yes. Toggle the refund modal to Partial and enter the amount. Partial refunds are available on Credit Card, Stored Card, and ACH transactions for both QuickBooks Online and QuickBooks Desktop integrations.

My customer was charged for technology fees. How does that work on a refund?

When you issue a partial refund, you can choose whether the refund includes the technology fee or not. Inclusive = you eat the fee, the customer gets it all back. Exclusive = the customer gets the principal back, the technology fee stays. Biller Genie also correctly prorates tax on the technology fee.

How long does the refund take to show up on the customer's card?

3 to 5 business days for credit cards, depending on the issuer. ACH refunds follow a similar window after settlement.

I refunded a payment but it's not showing in QuickBooks. Why?

For QuickBooks Online, refunds appear within minutes. For QuickBooks Desktop on MagicCarpet, refunds appear on the next sync cycle. If you're on QuickBooks Desktop v3, the bi-directional refund sync isn't available — see the upgrade-path note below.

Why is my refund showing as a single line in QuickBooks instead of the original line items?

The default behavior is to push refunds back with the original line items (proper GAAP). There's a failover to a single refund line if the original invoice items can't be matched — usually because they were modified or deleted in QuickBooks between the original payment and the refund.

Related articles

• Voids vs Refunds: When to Use Each
• How to Void a Payment
• Bulk Refunds and Bulk Voids
• Chart of Accounts: Mapping Your Accounts in Biller Genie