Automate VAT invoices for EU and UK orders, with a rule for who issues each one
Updated · By Ecomsellertool editorial team
To automate VAT invoices, first sort every order by situation: consumer or business, same country or cross-border, OSS or not, marketplace as deemed supplier or not, UK or EU. That decides who issues the invoice. Then pull the fields from Amazon's VAT report or Shopify, check the buyer's VAT number in VIES, and send exceptions to a person. Your adviser sets the rules.
- The European Commission requires invoices for most B2B supplies, but for B2C goods only in listed cases, such as distance sales taxed in another EU country without OSS (checked November 6, 2026).
- Under the EU's Union OSS scheme, a seller does not need to issue an invoice for intra-EU distance sales. If it issues one anyway, the rules of the country where it is registered for OSS apply.
- HMRC says a liable online marketplace should issue a full invoice, and an overseas seller need not invoice it for zero-rated deemed supplies (checked November 6, 2026).
- Amazon says an invoice is due for each shipment, not each order, and rejects an upload whose total or VAT differs from its own figure at two decimal places (checked November 6, 2026).
- Shopify's checkout VAT check runs through VIES and needs Shopify Tax. If VIES cannot validate the number, VAT is charged and there is no manual override (checked November 6, 2026).
- This recipe issues documents under rules your adviser approves. It files no returns and takes no tax position. Not tax advice.
The step map: who runs each step
Trigger: A shipped order or a refund on any channel, read from Amazon's VAT invoice data report at least twice a day and from Shopify and your other channels as orders change.
| Step | What happens | Who runs it |
|---|---|---|
| 1 | Rules read new shipments and refunds from each channel and put them in one queue: Amazon's VAT invoice data report, Shopify orders, and your other marketplaces and wholesale system. | Rule |
| 2 | Each order gets a situation from the decision table, using ship-from country, ship-to country, buyer type, the VAT number, your OSS status and whether the marketplace is the deemed supplier. | Rule |
| 3 | Orders the marketplace invoices are logged and closed. Orders with a buyer VAT number are checked in VIES or HMRC's UK service, with the result, date and time stored on the order. | Rule |
| 4 | Each invoice is built from the field map with your own number series and checked for empty required fields, line totals, and the VAT rate your approved table expects for that country. | Rule |
| 5 | Clean documents are issued in the template for that situation, uploaded to Amazon by shipment where it applies, and the channel's response is recorded against the invoice. | Rule |
| 6 | A person reviews the exceptions: a failed VAT number, a total Amazon rejected, a missing VAT registration, Northern Ireland or any situation the table does not cover. | Person |
| 7 | A refund opens a credit note that refers to the original invoice, and the case stays open until the credit note is issued and accepted by the channel. | Rule |
6 rule steps · 0 AI model steps · 1 person step. A rule follows fixed logic you approve; an AI model handles messy input and its output is checked by rules; a person makes the calls listed below.
What stays with a person
- The decision table itself, row by row, approved by your tax adviser before anything is issued
- Charging or removing VAT when a buyer's VAT number fails, or when a buyer disputes the result
- Reissuing or correcting an invoice already sent to a customer
- Whether to set up self-billing with a marketplace, and which countries need their own format
- VAT rates and product tax classes in the approved table, and every change to them
Which tools can run it
- Amazon's own invoicing option in its VAT Calculation Service, and Shopify's VAT invoices, where each one fits your orders
- An invoicing or VAT app, for a single channel with few exceptions, with its own rules and fees
- A workflow tool such as Zapier, Make or n8n that moves documents and VAT check results between channels and your accounting system
- Custom code on your accounts, for several channels, the decision table, one number series and one exception queue
Systems it connects
- Amazon SP-API (Reports and Feeds)
- Shopify (Shopify Tax and VAT invoices)
- VIES and HMRC's UK VAT number check
- Your other marketplaces and wholesale system
- Master record of VAT registrations and approved rates
- Your accounting system
Build size: Large
Building one invoice is simple. The work is the many order situations, country rules, several channels sharing one number series, and credit notes.
Picture a brand shipping into Germany, France and the UK (an illustrative example). A business buyer in France asks for an invoice without VAT. A German order went through Amazon. A UK customer wants a refund on an invoice someone typed by hand last month. Each of these has a different answer on who issues what, and a person working from a spreadsheet has to know them all. This recipe writes those answers down as rules, pulls the fields from each channel and leaves the unclear cases to a person. It is one page of our automation library.
Registration is a separate question. Our Amazon Germany guide and Amazon UK guide cover VAT registration, OSS, IOSS and who collects VAT. This page starts where they stop: the order has shipped, so what document does it need?
Who issues the VAT invoice for each kind of order?
This is the table to agree with your adviser before you connect anything. The "who issues" column comes from the official pages linked below it. The other columns are starting rules we suggest, for your team to change. A row applies to one order at a time, because the Commission's e-commerce notes say a marketplace's deemed supplier status is assessed per transaction (checked November 6, 2026).
| # | Order situation | Who issues the invoice | What the workflow pulls, and from where | What the workflow checks | When a person decides |
|---|---|---|---|---|---|
| 1 | EU consumer, same country as dispatch | You, if that country's rules or the customer require one. EU rules do not list this case | Order, ship-from and ship-to countries, VAT lines from Amazon's report or Shopify | Countries match; the country is on your national-rule list | Your adviser sets each country's rule once |
| 2 | EU consumer, cross-border, you use Union OSS | Nobody has to under EU rules. If you issue one, your OSS registration country's rules apply | The same, plus your OSS status from your master record | Destination VAT rate matches your approved table; the sale is reported as OSS | Whether to issue invoices at all, as a policy |
| 3 | EU consumer, cross-border, taxable in the destination country, no OSS | You must, under the rules of the country where the supply takes place | The same, plus your VAT registration in the destination country | A registration exists there; if not, stop | A missing registration goes to your adviser that day |
| 4 | Marketplace is the deemed supplier in the EU | Buyer side: the marketplace. It must invoice an intra-EU distance sale if it does not use Union OSS, and a domestic sale only if that country requires it. Your side: you invoice the marketplace for a supply inside the EU, or it self-bills | Ship-from country and your place of establishment; is-amazon-invoiced and invoice-status from Amazon's report | The order fits the deemed supply rule; you do not issue a second buyer invoice | Setting up self-billing, and any order the channel treats differently than you expect |
| 5 | EU business buyer with a valid VAT ID, goods crossing a border | You. No VAT charged; the invoice shows the buyer's VAT ID and the exemption or reverse charge wording your adviser approves | buyer-vat-number and is-business-order from Amazon's report; the Company VAT number from Shopify checkout | VIES says valid; the number is from a country other than dispatch; result and time stored | Name mismatches, and the wording used per country |
| 6 | EU business buyer with an invalid or unverified VAT ID | You. Usually with VAT charged at your country's rate | The same, plus the VIES response | Invalid is treated differently from "service unavailable", which retries | Any later request to remove the VAT, once the buyer proves its number |
| 7 | Refund or return on an invoiced order | Normally whoever issued the invoice. Amazon's status shows whether it created the credit note | transaction-type of RETURN or REFUND, transaction-id and original-vat-invoice-number from Amazon; the refund on the Shopify order | The original is found; the credit does not exceed it; rates match the original | Partial credits on mixed-rate orders, and reissues |
| 8 | UK consumer, overseas seller, sold through a marketplace, goods in the UK or a consignment of £135 or less | The marketplace, which should issue a full invoice. You need not invoice it for a zero-rated deemed supply | Channel, your establishment, goods location and consignment value | Your order record shows the sale as a deemed supply; no second invoice goes out | Northern Ireland orders, which have different rules |
| 9 | UK business buyer with a UK VAT number, overseas seller, goods in the UK, sold through a marketplace | You. The marketplace passes you the sale details, and you account for the VAT | The buyer's VAT number and sale details from the marketplace | HMRC's service confirms the number; your own UK registration is on file | A seller without a UK registration stops here and goes to your adviser |
| 10 | UK order on your own store, or a seller established in the UK | You. A VAT invoice to a VAT-registered customer, within 30 days of the tax point in normal cases | Shopify or your order system, with the buyer's VAT number if given | £250 or less can use a simplified invoice; zero-rated lines need no VAT invoice | Time limit extensions and anything outside normal rules |
The EU rows rest on three Commission documents. Its VAT invoicing page sets out when an invoice is compulsory (rows 1 and 3). Its e-commerce notes cover OSS and deemed suppliers (rows 2 and 4), including that the deemed supply from the seller to the marketplace inside the EU has to be invoiced, with self-billing allowed. Its invoicing notes give the basic rule that the country where the supply takes place sets the invoicing rules, with exceptions for cross-border reverse charge supplies and supplies taxed outside the EU.
For row 4, Amazon's announcement says it collects VAT for sellers not established in the EU on goods of any value shipped from EU stock, and on deliveries from stock outside the EU worth up to EUR 150 (checked November 6, 2026). For an import inside that limit, the notes say the seller has no EU invoicing duty to the marketplace, though a commercial invoice can still be needed for customs. Other marketplaces report this data differently, so map each one before you rely on it.
The UK rows come from HMRC's online marketplace guidance (last updated May 13, 2022), its guidance on goods sold directly to UK customers, where the seller issues the invoice, and VAT Notice 700, sections 16 and 18 (all checked November 6, 2026). Notice 700 adds that you need not issue VAT invoices to customers who are not registered, but in practice you will issue one to anyone who asks, and a retailer may face a penalty if a taxable person asks and gets none. One more UK case: on a consignment of £135 or less from outside the UK, the marketplace does not charge VAT when a business buyer gives its UK VAT number, and it can note on the invoice that the customer accounts for the VAT.
What fields does a VAT invoice need, and where does each one come from?
Build the invoice from this map, and make an empty required field stop the invoice. The field list is the Commission's for a full invoice, with HMRC's differences noted. The Amazon names are columns in its VAT invoice data report (checked November 6, 2026). Shopify's column describes where the value sits on the order.
| Required field | Amazon report column | Shopify or your own system | What to check |
|---|---|---|---|
| Date of issue | Set by your workflow | Set by your workflow | Not before the shipment |
| Unique sequential number | Your number; recorded as invoice-number | Your number series, per legal entity | No gaps or repeats across channels |
| Your full name and address | Your master record | Legal business name in billing settings | Name matches the VAT registration |
| Your VAT ID | seller-vat-number | VAT registrations in tax settings | Right number for the ship-from country |
| Customer's full name and address | billing-name, bill-address-1 to 3, bill-city, bill-postal-code, bill-country | Billing address on the order | Not empty; a simplified invoice may omit it |
| Customer's VAT ID, if the customer is liable for the tax | buyer-vat-number, buyer-company-name | Company VAT number from checkout | Valid check stored on the order |
| Description and quantity | product-name, quantity-purchased, sku | Line items | Description identifies the goods |
| Unit price without tax | item-vat-excl-amount ÷ quantity-purchased | Line price, without tax | Discounts shown, unless inside the unit price |
| Transaction date, if different | shipment-date | Fulfillment date | Your adviser confirms which date you use |
| VAT rate and amount | item-vat-rate, item-vat-amount, and the shipping, gift wrap and promotion columns | Tax lines on the order | Rate matches your approved table |
| Breakdown by VAT rate or exemption | Sum across those columns per rate | Sum across tax lines per rate | Lines add up to the total, to the cent |
| Reference to the original (credit notes) | original-vat-invoice-number, is-invoice-corrected | Your stored invoice number | The original exists and is not already credited |
| Conditional wording | Decided by the table row | Reverse charge note added by Shopify when the exemption applies | "Reverse charge" where the customer is liable; an exemption reference where exempt; "self-billing" where the customer issues it |
Three UK differences go in the template. HMRC also asks for the tax point, and the total VAT must be in sterling even when the rest of the invoice is in another currency. A simplified invoice for £250 or less needs your name, address and VAT number, the tax point, a description, and the total including VAT with the rate for each VAT rate; the customer has to agree. HMRC also says you can invoice in another language, as long as you can provide an English translation of a specific invoice within 30 days if an officer asks.
The Commission adds one limit that helps when someone asks you to add more to the template: once the listed information is on the invoice, a member state may not block the right to deduct VAT by requiring extra details. You may always add your own. National layers still exist elsewhere, though. Amazon's invoice guide says a recommended-invoice-format of XML means an Italian-established seller with a B2B customer in Italy must upload an XML invoice to Italy's Sistema di Interscambio.
How do you check a buyer's VAT number?
Check it once when the number appears on an order, and record the answer. Your Europe's VIES page says VIES is a search engine over national databases, not a database of its own, and recommends you keep track of your validation in case of a tax control (checked November 6, 2026). The stored record should show the number, the country, the result, the date and time, and the order it belongs to.
The result is more than a pass or fail, so each outcome needs its own rule.
| VIES outcome | What it can mean | What the workflow does |
|---|---|---|
| Valid | The VAT information exists | Stores the result; compares the name, if one is shown; moves to row 5 |
| Invalid | The number does not exist, is not active for intra-EU trade, or the registration is not final | Moves to row 6; tells the customer that its tax office can verify the number |
| Service unavailable | National databases can be down for backups | Retries later; does not treat this as invalid |
| Name does not match | National authorities will only confirm whether a given name and address is linked to a number | Holds the order for a person |
The rule behind rows 5 and 6 comes from Your Europe's cross-border VAT page: you do not charge VAT on goods sent to a business in another EU country if it has a valid EU VAT number, and if it does not, you should usually charge VAT at your own country's rate, with exceptions (checked November 6, 2026). The Commission's 2020 notes treat the customer's number, issued by a country other than the one the goods leave, as a substantive condition for the exemption. So a French number on goods shipped from France does not earn row 5.
For UK numbers, VIES is the wrong tool. GOV.UK's Check a UK VAT number service shows whether a number is valid and the registered name and address, and a VAT-registered business can use it to prove when it checked (checked November 6, 2026).
What do Amazon and Shopify already do for you?
Use the channel's own invoicing where it fits, then automate what is left.
Amazon. The VAT Calculation Service guide lists three options: let Amazon create invoices, use Amazon's tax data to create your own, or use your own tax data (checked November 6, 2026). It is available in ten European stores: Ireland, Spain, the UK, France, Belgium, the Netherlands, Germany, Italy, Sweden and Poland. If the first option suits you, most of this recipe collapses to rows 5, 6 and 9 for exceptions and a log of documents. Amazon marks those orders with is-amazon-invoiced and says the seller should not create invoices for them. Its report page describes the report as being for enrolled sellers who chose to upload their own invoices, so check what your account can see.
If you upload your own, a few rules shape the build. An invoice is due for each shipment, not each order. Amazon advises running the report at least twice a day, and the guide mentions a 24-hour SLA. Your TotalAmount and TotalVATAmount must match Amazon's to two decimal places or the upload is rejected, and it must be sent again. Uploads are limited to one every three seconds. When a shipment leaves a country where you have no VAT number on file, Amazon calculates nothing, the status is NoTaxCalculated, and you must work out the VAT and upload the invoice yourself. Send that status to a person as well, because it can mean a registration is missing. The reports need the restricted Tax Invoicing role.
Shopify. The VAT invoices page says invoices show on the order status page, and are not emailed automatically, while the EU tax page describes a setting to generate and send them (both checked November 6, 2026). The wording differs, so test it on your store. Orders from a third-party channel or app, orders with duties charged and orders shipping to Portugal are not covered, and invoices cannot be regenerated after an order changes. So credit notes and edited orders need their own step.
Shopify's VAT validation has its own limits (checked November 6, 2026). It needs Shopify Tax and an active fulfillment location in the EU, and it is not available on B2B-specific checkouts. The exemption covers EU-to-other-EU and EU-to-UK orders, not UK-to-EU or UK-to-UK. If VIES cannot complete the check, VAT is charged by default, with no manual override. That is the gap a workflow fills: a person has to handle the buyer who writes in afterward.
How should a refund become a credit note?
Treat a refund as its own document with its own status. Amazon's guide shows the states to watch: CreditNotePending when the money has gone back to the buyer, CreditNoteCreatedByAmazon when Amazon handled it, and CreditNoteRejected when your upload failed and has to be sent again. The upload uses DocumentType of CreditNote, which then also requires a TransactionId.
The content comes from the same two sources as the invoice. The Commission's page asks for a specific, unambiguous reference to the initial invoice and the details being amended. For UK supplies, Notice 700 says a valid credit note must reflect a genuine mistake, overcharge or agreed reduction, be issued within 14 days of the refund payment, and show the number and date of the original VAT invoice, the rate and amount of VAT credited in sterling, and the identifying details of both parties. The rate is the one in force at the tax point of the original supply, not today's. HMRC also says it will not make any repayment where a credit note misses these conditions, so a late or incomplete one has a real cost.
Refunds are also where channels drift apart. The same return can appear in a marketplace payout, in your accounting system and on the credit note, in different amounts and on different days. Have the workflow store the credit note number beside the refund, so whoever closes the month can match them. Our payout reconciliation recipe covers the money side.
What should stay with a person?
The table itself, first of all. A workflow should never decide a VAT treatment it has not been told about. When an order fits no row, the safe move is to stop and ask. After that, a person handles failed VAT numbers that a buyer disputes, invoices already sent that need correcting, self-billing with a marketplace, and any new country. Rates belong to your adviser too: this page lists none, because they change and your product class matters. For the country's product rules, our GPSR listing tracker is a separate job on the same markets.
Keep the records as well. HMRC says a marketplace must keep full records, including VAT invoices, for 6 years from the date of sale, and the Commission's OSS site has its own rules on records and invoices for the scheme (checked November 6, 2026). Ask your adviser what period applies to each entity, and keep the VAT check results with the invoices.
Who builds VAT invoice workflows for ecommerce brands?
Ecomsellertool builds workflow automation on your own marketplace and store accounts, and has built software on Amazon's seller APIs since 2017, shipping 50+ tools for 100+ teams. For this recipe we start with your channels, registrations and the table your adviser approves, then connect the reports, checks and one exception queue. Send a project brief below, or read how our workflow automation service works.
To be plain about proof: no case study we have published is a VAT invoicing project. Two are related building blocks:
- VAT calculation across marketplaces. Asinwiser combines sales analytics, repricing and VAT calculation in one Amazon tool, and handling the VAT differences between marketplaces was one of the hard parts of that build.
- Amazon financial data in one place. For SellerDrive we pulled Amazon's financial data into a profit and loss statement, with all fees shown.
We do not file returns or give tax advice; those stay with your licensed adviser. Custom parts can run on Ecomsellertool Growth OS. You keep your accounts, your data and the custom code we build; the Growth OS base is licensed to you.
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Frequently asked questions
Do I have to issue a VAT invoice for every order?
No. The European Commission says invoices are required for most B2B supplies but only for certain B2C sales, such as distance sales taxable in another EU country when OSS is not used. Some countries add their own rules for consumers. HMRC says you do not need to issue VAT invoices to customers who are not VAT registered, though in practice you issue one to anyone who asks. Ask your adviser which rules cover your orders.
Who issues the VAT invoice when Amazon is the deemed supplier?
The Commission's notes split it into two supplies. The underlying seller has to invoice the marketplace for a deemed supply inside the EU, and self-billing can be used. On the consumer side, the marketplace has no legal obligation to invoice an intra-EU distance sale under the Union OSS scheme, but must if it does not use that scheme. In the UK, HMRC says the marketplace should issue the invoice.
What happens if a buyer's VAT number fails in VIES?
Your Europe says that if a customer has no valid EU VAT number, you should usually charge VAT at the rate for your country. An invalid result can also mean the number is not active for intra-EU trade or the registration is not final, and the customer can ask its tax office to check. If the system is down, retry later. Keep a record of each check.
Can Shopify create VAT invoices automatically?
Yes, with limits. Shopify's help pages say VAT invoices need Shopify Tax, an EU or UK destination, and no duties charged on the order, and that orders from a third-party channel or app and orders shipping to Portugal are not covered. Invoices cannot be regenerated after an order changes, so edits and refunds need their own step.
What must a credit note show?
The European Commission lists a specific, unambiguous reference to the initial invoice and the details being amended. HMRC's Notice 700 asks for the identifying number and date, both parties, a description, the quantity and amount, the total credited excluding VAT, the rate and amount of VAT credited, and the number and date of the original invoice. It also says to issue it within 14 days of the refund payment.
Does this software decide my VAT treatment?
No. The workflow applies a table that you and your tax adviser approve, and it stops when an order does not fit a row. We build the operations and integration layer. VAT registration, rates, returns and any position on a particular order stay with your adviser. This page is general information, not tax advice.
