If your store uses prices that include VAT, you need to turn on a setting in Markets in order for tax-exempt customers to not be charged VAT at checkout.

Open your store's Settings and go to Markets, then click on Preferences:

In Markets Preferences, enable the checkbox Include or exclude tax based on your customer's country:

Then save the settings. Now, when a tax-exempt customer goes to checkout they should see VAT getting deducted from the total.

Note: The VAT only gets deducted from the checkout total once the customer has entered a shipping address. Before an address is entered, the price will still reflect VAT.

If you are using Shopify Tax and Shopify is charging tax-exempt customers taxes, you need to contact Shopify Support to get this resolved as you don't have direct control over how Shopify calculates taxes.
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