I appreciate you for posting your concern in the Community, @Calvds. I have information concerning the transactions showing the invoice is exempted from VAT in QuickBooks Online (QBO).
Tax rates can be changed and will depend on where you ship your products or perform services at your customer’s address. Thus, you can check your customer’s setup, particularly the billing address and shipping address.
Once certain that the customer’s setup is correct and the location where the service is performed is not exempted from tax, I recommend you manually categorise to add the VAT percentage to the transaction.
Here’s how:
- Go to the Banking menu and navigate to the Bank tab.
- Locate the transaction where the invoice is reflected as exempt.
- Click the transaction to expand and add the VAT percentage from its designated section.
- Enter the other necessary details to categorise the transaction and tap the Add button.

For your reference, you can view this article to learn more about setting up and using the VAT feature in QBO.
If you’re done sorting out your transactions, you can start categorising the other transactions and reconciling them to avoid any discrepancies at the end of every period.
Feel free to add any other concerns you may have here. I’ll ensure you get the assistance you need. Have a good one!