I’m using Link My Books— is it still accurate?
Yes, Amazon still effectively deducts VAT from UK sales even after you are VAT registered, because Amazon collects VAT from the customer and only pays you the net amount excluding VAT. This is normal and expected.
Being VAT registered does not stop this deduction. Amazon also charges VAT on its seller fees, which is deducted from your settlements. You are not losing that VAT permanently because you can reclaim the VAT on Amazon fees as input VAT on your VAT return.
Link My Books remains accurate as long as it is correctly configured and pulling the correct Amazon tax and settlement reports. You should make sure your VAT number is correctly entered in Seller Central and that VAT Calculation Service is enabled if you are using it.
You should also check that Link My Books is set to treat sales VAT as output VAT and Amazon fee VAT as reclaimable input VAT. If those settings are correct, the numbers you see are usually right.