Payrix Refund: 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 realizing 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:

Step 1: Submit a refund request to Payrix

The refund can only be processed by requesting to Payrix (AU:; US:

  • The refund can be partial or full.
  • The refund must be to the same Credit Card.

The following information must be provided to Payrix:

  • Transaction Number
  • Amount to be refunded
  • Date
  • Reason for Refund requests
Step 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.
Step 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 the 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 -FAQ- How to automatically cancel scheduled transaction when the invoice is modified in the Accounting Package

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