It is a trend in online selling to try and store your goods in a warehouse or distribution centre as close to your customers as possible. The Amazon FBA solution allows sellers to make use of their fulfilment centres spread across the continent, but sellers can also employ other third party fulfilment solutions or even use their own warehouses.
Whilst having your goods close to your customers obviously enhances the buying experience – allowing expedited deliveries – and can reduce your costs of complexities of delivery, the place of supply rules in the EU state that a business must register for VAT in any country from whence they fulfil commercial orders.
If you import the goods into the EU to store in these distribution centres (for onward sale) you will generally be required to pay import VAT (and possibly import duty) to the tax authority where the goods are imported. You will be required to register for VAT when you store goods in the EU country and you are therefore able to claim back this import VAT via this registration.
Having the VAT registration in each country of distribution doesn’t necessarily mean you should charge VAT on all sales, nor should you necessarily charge the VAT of the country of fulfilment.
Read more about Business-to-Business sales or Distance Selling for more explanation