Yes, as long as you make a European shipment (except the Canary Islands, Ceuta and Melilla) the VAT will be applied.
Remember that if you have used a VIES VAT number, VAT will not apply to intra-community transactions. For more information, please refer to the article VIES: What is it and how do I register?
In our Help Center you can also find all the instructions you need to download your invoices.