Fees are created as products in your store. To make sure taxes are not charged on your fees, you’ll need to update the settings for each fee product.
In your Shopify admin, go to Products.
Search for the fee by name, or filter your products by Product Type “Fee.”
Open the fee product you want to update.
Under Pricing, uncheck “Charge tax on this product.”
Click Save.
This will stop taxes from being added to your fees.