FAQ- How to Refund When An Invoice Has Been Paid Twice

You may face a situation when the same invoice gets paid twice using different payment methods.


A payment was made by credit card and applied to the invoice, not realising that an Automatic Payment was being processed/settled at the same time. This results in the following errors:

  • There are accounts with unprocessed or unmatched payments
  • Payments can only be applied to Invoices that are awaiting payment.  The invoice is either fully paid, draft or has been voided.

How do I fix it?

The following diagram describes the steps involved in issuing a refund and correcting accounts:

1. Process a refund of the amount to the payer either through IntegraPay or Bank Transfer

Use your payment processor merchant such as IntegraPay to complete this step. 

Follow these steps to process a refund through the IntegraPay console:

  1. Log in to IntegraPay.
  2. Search the transaction and click Refund to refund an amount for that transaction.
    If you don't see this option, your account doesn't have permission to process Refunds.
  3. On the Refund Transaction screen, click Partial Refund, and specify the amount to refund.
    Ensure that you have deducted the surcharges paid while processing the incorrect invoice.
  4. Enter your email in the Email Receipt To text area and click Refund Transaction to refund the amount.
    IntegraPay automatically adjusts the next invoice with the refunded amount.

2. Remove the payment from Xero and sync payments

It is recommended that payment is removed from the invoice in your accounting package and ConnectWise, using the following steps:

  1. Log in to Xero and search the incorrect invoice for which a refund is required.
  2. Click the Payment link on the invoice to see the Transaction: Payment page.

  3. Select Options > Remove & Redo to remove the payment from the invoice.
    This should remove the payment, and you should see the appropriate success message.
  4. Log in to Wise-Sync and sync payments to change the payment of the invoice to 0. If you don’t sync payments, the payment will remain in ConnectWise.

3. Apply a payment for the invoice and sync payments

As you have removed the payment from the invoice, you need to receive the correct payment to settle the account. The received payment would then be synced back to ConnectWise through Wise-Sync. Follow these steps:

  1. In Xero, search and open the invoice and go to the bottom end of the Invoice
  2. In the Receive a payment section, enter the correct amount and the date. Ensure that you have selected the Wise-Pay Clearing Account in the Paid To drop-down.
  3. Click Add Payment to receive payment for this invoice.
  4. Go to Wise-Sync and sync payments to reflect the payment in ConnectWise.

How can I avoid this error in future?

Configure Wise-Pay to Check Updated Payments, Wise-Pay will cancel an automatic payment, if the invoice has been fully paid. If the invoice is partially paid, the automatic payment would be rescheduled for the remaining amount.

Follow the steps outlined in this article - Check scheduled bank debits against invoice due balance prior to the day of payment

Simone is the author of this solution article.

Did you find it helpful? Yes No

Send feedback
Sorry we couldn't be helpful. Help us improve this article with your feedback.