Received on invoice 0% VAT exempt

Dear Sir/Madam, I am VAT exempted, so my purchase invoices must include 21% VAT. However, I have my webshop through Shopify, for which I pay a monthly subscription fee. These invoices contain 0% vAT, but Shopify refuses to charge me 21% vAT. How do I process this here in my accounts? Because I do, of course, have to pay vAT on this. So, should I do a special vAT declaration for here? Or is it best not to include this here in my accounts?