Welcome to the Community, LB_HLT. We're focused on turning your experience around and recognize the significance of precise financial reporting, particularly for handling tax exemptions. Sales tax calculations in QuickBooks Online (QBO) are automated. In your situation, it's essential to adjust the sales tax settings in the Shopify connector. I'll guide you through the process of doing such.
You can manage settings for tax calculations on your products, such as including taxes in prices, charging VAT on digital goods, and applying tax to shipping. These settings are found on the Taxes and duties settings page. For more information, refer to Tax overrides and exemptions.
Here's the Steps:
- From your Shopify admin, go to Settings > Taxes and duties.
- In the Decide how tax is charged section, select the options that apply.
- Click Save.
After which, I recommend contacting Shopify connector support for more specialized assistance with configuring the tax exemption. You can contact them using the provided phone number.

For more information, refer to this article: Learn how QuickBooks Online calculates sales tax.
Additionally, I'm providing a link to an article that guides you on how to modify your sales tax details in QBO. This will assist you in updating your taxes to ensure the correct amount is collected: Edit Sales Tax Rate.
Managing tax exemptions properly ensures compliance and smooth operations for your business. Should you require further assistance on this matter, please do not hesitate to reach out. Have a nice one.