Syncing Sales Tax in Shopify orders with QuickBooks Online

Written by the MyWorks Team

Updated at May 29th, 2024

MyWorks makes it as easy as possible to handle accounting for the sales tax collected in Shopify. We'll automatically sync the tax charged on the order into QuickBooks Online as we sync the order: no setup needed on your part!

MyWorks is perfectly compatible with the automated Shopify Tax service in Shopify. When enabled in Shopify, MyWorks will sync the accurate sales tax collected on the order into QuickBooks.

When using Automated Sales Tax in QuickBooks Online (US) 

If your QuickBooks Online company is in the United States, you likely have Automated Sales Tax enabled. The Sales Tax collected in the Shopify order will be passed into the "Sales Tax" subtotal field in QuickBooks Online. This will always match what's collected in the Shopify order, and you can use reporting in QuickBooks Online to report on sales tax collected. 


When using Manual Sales Tax in QuickBooks Online (outside of US) 

If your QuickBooks Online company is outside of the United States, you likely manage tax rates manually in your QuickBooks Sales Tax tab. 

MyWorks allows you to easily map your Shopify sales tax rates to the sales tax rates present in your QuickBooks company. There are two areas in MyWorks to manage this. 

Settings > Tax

In MyWorks Sync > Settings > Tax, you can set your QuickBooks tax rate that should be applied to non-taxable orders: orders that are not charged tax. This is normally a tax rate named “Out of Scope”, or “Exempt”.


Map > Tax Rates

In MyWorks Sync > Map > Tax Rates, you can view your Shopify tax rates and select the matching QuickBooks tax rate for each.  

  • Country level rates will be shown first at the top, like GST in the below example.
  • Any province or state - level rates will be shown next, like in the below example.

MyWorks also supports compound mapping, like in the below example where GST + QST would be charged in the same order - to map these rates in Shopify to the correct combined rate in QuickBooks.

Syncing tax as a line item

If you enable the setting to sync sales tax as a line item in MyWorks Sync > Settings > Tax,  the Sales Tax collected in the WooCommerce order will instead be passed into a line item in QuickBooks Online. This "Sales Tax" item is set in MyWorks Sync > Settings > Tax - and can be created in your QuickBooks and assigned to your "Sales Tax Payable" account.