QuickBooks Desktop Chargeback Reconciliation
How to reconcile chargebacks in QuickBooks Desktop using the built-in Record Bounced Check function.
QBD partners only: This guide applies exclusively to partners using the QuickBooks Desktop integration. If you are on QuickBooks Online, Alternative Payments handles chargeback reconciliation automatically — no manual steps are required.
When a chargeback occurs on a payment that has already been synced and deposited, QuickBooks Desktop requires a manual reconciliation process. Unlike QuickBooks Online, where Alternative Payments manages this automatically, QBD partners need to update their books directly within QuickBooks Desktop.
The Previous Manual Process
Before the streamlined method described below, the recommended approach involved three separate steps:
Unlink the payment from the invoice — remove the association between the received payment and the original invoice in QBD.
Create a journal entry — debit the Accounts Receivable account and credit the Chargebacks account to record the chargeback amount.
Link the payment to the journal entry — re-associate the payment record with the journal entry created in step 2.
While this approach works, it is time-consuming and prone to error. The method below achieves the same result in fewer steps using a built-in QuickBooks Desktop feature.
Recommended Process: Record Bounced Check
QuickBooks Desktop includes a built-in Record Bounced Check function that provides a cleaner, fewer-step alternative for recording chargebacks. The steps below walk you through the full workflow.
Step 1: Locate the Original Payment
In QuickBooks Desktop, open the Customer Center (from the top menu, go to Customers > Customer Center).
Find and select the customer associated with the chargeback.
In the customer's transaction list, locate the original payment that was received and is now being disputed.
Double-click the payment to open it.
Step 2: Use the Record Bounced Check Function
With the payment record open, click the Record Bounced Check button in the toolbar at the top of the payment window.
Note: The Record Bounced Check button appears in the toolbar of the Receive Payments window. If you do not see it, confirm that the transaction you have open is a received payment (not a deposit or invoice).
A Manage Bounced Check dialog will appear. Fill in the following fields:
Bank Charge Amount: Enter any bank fee associated with the chargeback, if applicable. If there is no fee, enter
0.00.Date: Confirm or update the date of the chargeback.
Expense Account: Select the account you use to track chargebacks (for example, your Chargebacks account).
Class: Assign a class if your company uses class tracking; otherwise, leave blank.
Click Next to proceed.
Step 3: Review and Confirm the Resulting Transactions
QuickBooks Desktop will automatically create the following records on your behalf:
A debit memo (or invoice) that re-opens the original invoice for the chargeback amount, restoring the balance owed by the customer.
A journal entry that debits Accounts Receivable and credits the expense account you selected (your Chargebacks account), recording the chargeback against your books.
Review the summary shown in the dialog to confirm the amounts are correct, then click Done (or Finish) to save the transactions.
Step 4: Verify the Customer's Balance
After completing the steps above:
Return to the Customer Center and select the affected customer.
Confirm that the original invoice now shows an open balance equal to the chargeback amount.
Confirm that the chargeback is reflected in your Chargebacks account register (Lists > Chart of Accounts > open the Chargebacks account).
The customer's account is now accurately updated to reflect the disputed payment, and your books are balanced without the need for manual journal entries.
Summary: Old Process vs. Record Bounced Check
Steps required
3 (unlink payment, create journal entry, re-link payment)
2 (open payment, use built-in function)
Journal entry
Created manually
Created automatically by QBD
Risk of error
Higher — manual debit/credit entry
Lower — QBD calculates entries
Accounts updated
Accounts Receivable + Chargebacks
Accounts Receivable + selected expense account
If you need further assistance, don't hesitate to reach out to our Customer Experience team at customersuccess@alternativepayments.io or by sending us a message via the Live Chat within your partner dashboard.
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