Here's how to tag a bank transaction as a sale, or purchase, of goods or services outside the UK but within the EU.
Before you can tag these transactions as EU, you need to enable the VAT reporting in FreeAgent.
To do this, click Settings at the top right of the screen, then click VAT Registration.

Make sure the "Enable EC VAT Reporting" box is ticked.

Save your changes.
As you explain the transaction, you have the option to tick whether it's not from the EC, whether it relates to EC Goods, or EC Services.

Tick the appropriate box to tag the transaction.
Some transaction types can't be tagged, for example invoice receipts, because in that case it's the invoice that you tag.
That depends on the tag and the circumstances. Please note that UK transactions count as "Non-EC".
If you tag a Money In transaction as EC Goods, and you're allowed to zero-rate that sale of goods according to HM Revenue's rules, then as well as tagging the transaction as EC Goods, you need to set the VAT rate as 0%.
If you do this correctly, and you're not on the flat rate scheme, FreeAgent won't put any VAT in box 1, but would add the amount of the receipt to boxes 6 and 8 of your VAT return.
And if you're on the flat rate scheme, this receipt would be treated as part of your flat rate turnover and have flat rate VAT worked out on it, which would go in box 1. Boxes 6 and 8 would also contain the amount of the receipt.
If you tag a Money Out transaction as EC Goods, FreeAgent will assume that there's acquisition tax on those goods and that box 2 needs to be filled in. For this to work, you need to set the VAT as either 0% or Auto.
It'll work out the VAT that you would have paid on those goods if you'd bought them in the UK, depending on which category you've put the transaction into.
It'll then put that amount into box 2, and also into box 4 so that you don't pay any extra VAT on those goods.
Finally, it'll add the amount of the payment to boxes 7 and 9 of your VAT return.
Purchases of EC goods are reported the same way whether or not you're on the flat rate scheme.
If you tag a Money In transaction as EC Services, this sale is outside the scope of UK VAT, according to HM Revenue's rules on the place of supply, so you need to set the VAT rate as N/A.
So it won't put any VAT in box 1.
But it will put the amount in box 6 if you're not on the flat rate scheme, even though usually sales outside the scope of VAT don't go in here, because HM Revenue specify that sales of services to the EU do go into box 6 - unless you're on the flat rate scheme, in which case sales of EC services won't be in box 6 because they're not part of your flat rate turnover.
If you tag a Money Out transaction as EC Services, you also need to set the VAT rate as 0%, so that FreeAgent doesn't reclaim input VAT. Don't use Auto VAT or any of the other rates.
Nothing will appear in box 2 or box 9 of your VAT return, because those boxes are just for goods.
If you're using the flat rate scheme, FreeAgent won't put the amount of this cost into box 7 of your VAT return, but if you're not on the flat rate scheme, the cost will appear in box 7 of your VAT return.
FreeAgent can't yet work out the reverse charge on these services.
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