Reconciling Xero invoices paid through Square

Pamela Calilung
Customer success manager Request support


  • Learn how to reconcile an invoice in Xero that is paid Square via virtual terminal, register, terminal or reader.

If you create invoices in Xero for each Square transaction, turning off the Sales Sync of the Square and Xero integration is recommended so that the sales will not double up.

Turn off sales sync

  1. Sign in to your Amaka integrations account.
  2. Click the integration you would like to update.
  3. Go to the Features page and toggle off the Sales Sync and then click Save and Continue.

You need to turn on at least one module which is the Payment Service. The payment service allows your customers to pay your invoices through Square’s online payment service. It also allows the integration to sync the transfers that Square has made to your bank account and the Square fees.

If you invoice from Xero and accept payments through any Square device or virtual terminal, you need to mark the invoice as paid by adding a payment. Just allocate the payment to Square Balance account.

The integration syncs the Square deposit and Square Fee so you can easily reconcile the Square transfer and click ok on the matching bank transfer transaction.

Need any help?
If you have questions about the procedure, visit our Help desk.