Syncing Sales Tax in WooCommerce orders with QuickBooks Desktop - United States

Learn how to efficiently sync sales tax from WooCommerce orders with QuickBooks Desktop for accurate financial management.

Written by the MyWorks Team

Updated at January 23rd, 2026

Table of Contents

Using An Automated Sales Tax Service in WooCommerce: Manually mapping sales tax rates in WooCommerce

MyWorks makes it as easy as possible to handle sales tax accounting in WooCommerce. We'll automatically sync the tax charged on the order into QuickBooks Desktop as we sync the order; no setup required on your part!

In the US, Myworks Sync will work with any automated sales tax service (like WooCommerce Tax or Avalara) - or manual rates you configure in WooCommerce.

Using An Automated Sales Tax Service in WooCommerce:

When an automated sales tax service is used in WooCommerce, MyWorks Sync supports syncing these calculated rates within the taxed orders synced from WooCommerce to QuickBooks.

This would occur as a line item in the order in QuickBooks, as it's not possible to map automatically generated rates in WooCommerce to the static rates that would be present in the QuickBooks item list. This approach results in the total tax collected being accurately recorded in QuickBooks, and reports from your automated tax service can be used to see a breakdown of tax by region.

What's needed:

In MyWorks Sync > Settings > Tax, set the taxable and non-taxable codes to "Tax" and "Non", respectively.
In MyWorks Sync > Settings > Tax, enable the setting to sync tax as a line item, and choose a sales tax item in QuickBooks for both the line item and tax rate option: these must be different rates.

You can see this configured in the screenshot below:

Under these circumstances, our sync will sync WooCommerce orders taxed with the correct amount into QuickBooks Desktop, as a line item. The “QuickBooks Sales Tax Rate” should set to a 0% rate in QuickBooks as the Sales Tax is accounted for in the line item.=

For more information, we have an excellent doc on handling automated sales tax with QuickBooks Desktop here.

Manually mapping sales tax rates in WooCommerce

When using manual rates in WooCommerce, your tax rates must be set in your WooCommerce settings, then added as Sales Tax Items in your QuickBooks Desktop Item List. Once added in both WooCommerce and QuickBooks, they can be mapped together in MyWorks Sync.

What's needed:

In MyWorks Sync > Settings > Tax, set a taxable and non-taxable code - normally "Tax" and "Non". The tax code format should remain set to "Sales Tax Item".