Many site admins have asked me, “How do I set up taxes in Magento now that the UK is leaving the EU?” First and foremost, you can leave it how it is for the moment. In the coming months and years the changes will come. The change mainly affects sites that have a large volume of orders coming from EU countries outside of UK.
Eventually there will be more paperwork required for import and export duties. This could cause shipping delays if the paperwork is not completed in a timely manner. VAT will still be charged on all retail sales but Business to Business sales may need some adjustments. As it is, if you are VAT registered then you can waive the VAT for B2B sales. This could change when the UK leaves the EU. There is, however, a potential upside to this. The UK will no longer be required to adhere to EU tax law and can set their own VAT which could be lower than their competitors in nearby countries.
The main idea here is that any changes can take up to two years to go into effect. That will give business owners enough time to work out any foreseen changes to shipping and tax setups on their sites. WATCH THIS SPACE.