If you sell on Amazon and on your own Shopify store, your VAT returns are built from at least two exports, and often a third one from your payment provider. Each export is correct on its own. Put together carelessly, they can count the same sale twice, put one sale in both your OSS return and a local return, or hide the fact that you crossed the €10,000 threshold long ago.
This guide shows where double-counting happens, the one rule that prevents it and a routine you can run every month.
The rule: every order counted once, in one place
Every sale belongs to the channel where the customer bought and paid. How it is taxed does not depend on the channel. It depends on where the goods ship from, where they go, whether the buyer is a consumer or a business, and who is responsible for the VAT. The channel tells you where to find the order. The VAT rules tell you where to declare it.
Five places where sales get counted twice
1. Order exports plus payout reports
Your Shopify orders export and your Shopify Payments or PayPal payout report describe the same sales. Use the orders as the source for VAT. Use the payouts only to check that the money arrived.
2. Shopify orders fulfilled by Amazon
If you use Amazon’s Multi-Channel Fulfilment to ship Shopify orders, check whether those shipments also appear in your Amazon VAT data. If they do, count each order once, from the channel where the customer paid.
3. The same sale in OSS and in a local return
A sale from stock in one country to a customer in the same country is a domestic sale: it goes in that country’s local return. A sale shipped from one EU country to a consumer in another is a distance sale: it goes in your OSS return if you use OSS. The same order never belongs in both. This happens most often to sellers who store goods in several countries.
Remember too that OSS is all or nothing: once you are registered, all your eligible distance sales go through OSS, from every channel. You cannot put your Shopify sales in OSS and declare the same kind of Amazon sales in local returns.
4. Sales where Amazon collects the VAT
When Amazon is the deemed supplier, Amazon pays the VAT on that sale. If the same sale also ends up in your own return, the VAT is paid twice.
5. Refunds
A refund can show up in your orders export, as a negative line in your payouts and as a credit note you entered by hand. Take refunds from one source only.
One more mistake looks like double-counting without being it: treating gross amounts as net. If the VAT included in your prices is counted as sales, your taxable amounts are inflated by exactly that VAT.
The €10,000 threshold counts all your channels together
The EU-wide €10,000 threshold for cross-border sales to consumers applies to your total: all channels and all EU countries together. Being under €10,000 on Shopify and under €10,000 on Amazon does not mean you are under the threshold. And it stops protecting you altogether once your goods ship from more than one country. Our guide to EU VAT thresholds and multi-country storage explains when it applies.
A simple monthly routine
| Source | Use it for | Do not use it for |
|---|---|---|
| Amazon VAT Transactions Report | Amazon sales, refunds and stock transfers | Payouts or fees |
| Shopify orders export | Shopify sales and refunds | Orders Amazon also shipped, if they already appear in Amazon data |
| Payment provider payouts | Checking the money arrived | VAT returns |
- Export each source for the same period, by transaction date.
- Remove duplicates by order ID across all sources.
- Tag every order with where it shipped from, where it went, consumer or business, and who is responsible for the VAT.
- Route each order: local return, OSS return, intra-Community supply without VAT, or excluded because the marketplace pays the VAT.
- Check your running total of cross-border sales to consumers against the €10,000 threshold, all channels together.
- Take refunds from one source and file them in the period you made them.
How hellotax helps
Our VAT software combines Amazon, Shopify and other platforms in one place, so each order is counted once and routed to the right return. See how we did it for a German Amazon and Shopify brand, or book a free consultation to review your own setup.
FAQ
Do Amazon and Shopify sales go in the same VAT return?
Yes, when they are the same kind of sale in the same country. Returns are organised by country and VAT treatment, not by sales channel.
Is the €10,000 threshold per marketplace?
No. It covers your total cross-border sales to consumers in the EU, across all channels.
Can I use OSS for Shopify and local returns for Amazon?
Not for the same type of sale. Once you are registered for OSS, all eligible distance sales go through it. Domestic sales from local stock still go in local returns, whatever the channel.
Should I use my payout report for VAT?
No. Payouts include fees and timing differences. Use order and transaction data, and use payouts only to check payments.
The post Amazon & Shopify VAT Reporting: How to Avoid Double-Counting Sales appeared first on Hellotax Blog.
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This articles is written by : Nermeen Nabil Khear Abdelmalak
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