You now have the ability to override QuickBooks Online Sales Tax with the Sales Tax from your Shopify online stores and Shopify POS! This update will resolve any rounding issues you may have between Shopify and QBO related to Sales Tax, and we encourage you to implement this new capability (however it is essential you consult your accounting professional prior to making any adjustments).
To configure using or not using Shopify Sales Tax in place of QBO Sales Tax, start by enabling the feature. From your weintegrate account, click the gear on the top right, select Preferences from the dropdown menu, and then click the General settings link.
To start having weintegrate replace QBO Sales Tax with Shopify Sales Tax, click the checkbox to enable Override Accounting Transactions with Sales Channel Taxes
When selecting to use Shopify Sales Tax, you will also be required to use Override Accounting System Ship From with Sales Channel Ship From. You can learn more on managing this here.
Important: How to Configure Shipping Tax
Once you enable weintegrate to replace QBO Sales Tax with Shopify Sales Tax, you must map Shipping Fees from Shopify to a line item on QBO Sales Receipts (and Refund Receipts).
Create a Product in QBO for Mapping Shipping Fees from Shopify
Set a QuickBooks Online Class to Shipping Fees by Store Connection