How Storing Stock in EU or the UK Affects Your Amazon FBA and Shopify VAT Obligations

Key takeaways

Storing inventory in any EU country or the UK for Amazon FBA or Shopify creates specific VAT registration and tax reporting requirements in each location. Keeping up with filing, tracking stock movements, and setting up correct VAT rates helps avoid surprise fines and keeps sales running smoothly.

Key points:

• Storing goods in a country almost always requires registering for VAT there, even if you use a 3PL or Amazon FBA.
• You should report both sales and physical movements of stock (even without a sale) across EU/UK borders using the right filings.
• VAT on sales is based on the customer’s delivery country, not your warehouse location.
• Shopify helps automate VAT collection but does not handle VAT registration, filings, or stock movement tracking.
• Regular reviews, careful record-keeping, and timely updates to systems prevent most VAT compliance issues.

Moving inventory into an EU country or the UK for Amazon FBA, or using a 3PL, creates new VAT registration and tax filing requirements. For e-commerce sellers, these VAT obligations can seem confusing, especially when selling across both Amazon and Shopify. For more on how Amazon FBA warehousing sites affect VAT, see our post on Amazon FBA Warehouses in Europe. By understanding stock movements, EU rules, and correctly configuring Shopify Tax Compliance, you can avoid tax penalties and keep your business running smoothly.

Who Needs to Pay Attention to Warehouse VAT Rules

Amazon FBA, 3PL, and Shopify sellers who store products in the EU or UK should pay careful attention to their VAT requirements.

Answer-first: If you store inventory in a country—even without an office—local VAT registration and ongoing compliance become mandatory.

This is true whether you use Amazon FBA, another fulfillment provider, or your own foreign warehouse. The location of your goods creates a tax nexus in almost every country where they are stored.

At 1stopVAT, we help sellers who use both Amazon FBA and Shopify across Europe and the UK. Many have felt overwhelmed at the start, but our team’s hands-on guidance makes VAT registration and ongoing tax filing manageable—even if stock moves frequently or is held in multiple countries.

Why Your Stock Location Matters for VAT

Answer-first: Storing goods in any EU or UK warehouse almost always triggers a need for VAT Registration in that country.

Whenever you store inventory in a country, even if you use Amazon FBA or a third-party logistics (3PL) provider, you create a VAT obligation there. This is backed by recent research and strict European tax guidelines.

• Amazon FBA accounts as consignment stock in tax law. VAT Registration is mandatory in each country where inventory rests.
• Using a 3PL or storing products on “call off stock” terms? If you control the goods and ship to known customers, you might not need to register—but in most cases, local authorities treat it as a consignment, and you should register.
• Selling into multiple EU markets? Each warehouse location usually means a new VAT Registration.

You can check country-by-country details, but as a rule, anything more than a temporary, token amount of stock will trigger these obligations.

UK: EORI Number Adds Another Step

If you store stock in the UK, you’ll need an EORI number in addition to the local VAT number. This applies even if you’re a non-UK business.

VAT Registration Requirements for Amazon FBA and 3PL Warehousing

Answer-first: You should register for VAT in every EU or UK country where your goods are warehoused for sale.

Here’s how this works:

• Consignment Stock (most Amazon FBA/3PL setups): Requires a local VAT Registration and ongoing compliance. The warehouse operator has control, so the tax authorities treat the transfer of inventory as a supply, making local VAT registration non-negotiable. Source
• Call Off Stock: If you use a program that keeps inventory under your control and moves it to the customer only when a sale occurs, you may not need a separate VAT registration—a rare scenario.
• Intrastat and EC Sales Listings: If you move stock between EU countries (e.g., from France to Germany), you need to report these intra-EU stock movements using specialized filings.
• Different Countries, Different Numbers: Each separate country where you warehouse means a separate VAT number and, often, local filings.

At 1stopVAT, our clients are often surprised by how simple “expanding storage” in a new EU country can be, yet how much paperwork it triggers. But with our support, the step-by-step process quickly makes sense, from first VAT application to registering your EORI number and compiling the right stock movement paperwork.

Checklist

• Obtain VAT Registration in each warehouse country.
• Register for an EORI number in the UK.
• Set up Intrastat and EC Sales List filings if shipping between EU states.
• Keep accurate transfer and inventory records.

Ongoing Warehouse VAT Compliance and Reporting

Answer-first: Once registered, you should maintain your VAT number(s), file returns, and keep detailed records of all stock movements and sales.

Warehousing triggers VAT filing, but it does not end there. Your ongoing obligations include:

• Regular VAT returns: Based on local country deadlines, detailing every sale and stock movement.
• Intrastat reporting: Necessity to follow local reporting thresholds(for imports and exports separately).
• Record-keeping: Full details of receipts, shipments, inventory, and warehouse exits.
• EC Sales Listings: Reports for B2B cross-border transactions.
• Supporting documentation: Tax authorities can request paperwork for any intra-EU stock movement, sales invoice, or country transfer.

We tell clients: Treat warehouse stock movements just as seriously for taxes as your actual sales. All of these records help you avoid time-consuming audits and unexpected fines.

Calculate VAT on Your Amazon FBA and Shopify Sales

Answer-first: The correct VAT rate depends on your customer’s location, their business status, and the method of delivery.

The three essentials for Amazon FBA and Shopify VAT compliance:

• B2C (Consumer) Sales: VAT is calculated at the rate of the customer’s delivery country—not the origin of your warehouse.
• B2B (Business) Sales: Reverse charge rules often apply. You do not charge VAT; the buyer self-assesses (provided their VAT number is valid). More guidance here
• Cross-border sales from your warehouse: If you ship to other EU countries, the One-Stop-Shop (OSS) program lets you report and pay VAT centrally. But local compliance must still be maintained for stock movement.

A common mistake: Thinking that the warehouse location sets the VAT rate. Always charge VAT according to the customer’s country.

At 1stopVAT, we often spot sellers on Shopify who’ve set only their home country’s VAT rate. After fixing these settings and clarifying OSS eligibility, they avoid massive underpayment penalties and feel more secure during audits.

Setting Up VAT in Shopify for Multi-Country Tax Compliance

Answer-first: Shopify handles VAT calculation, but you should configure VAT registration numbers and rates for each country where stock is stored and sold.

Here’s how we help clients set up Shopify Tax Compliance:

1. Enable VAT collection in Shopify. Add tax rates and registration numbers for all countries where you warehouse or have a VAT registration.

2. Configure location-based rules so VAT is calculated by customer delivery country, not warehouse origin.

3. Keep off-Shopify records. Shopify does not handle VAT registration or filings. You need an outside system (or accountant, or 1stopVAT’s portal) to track returns, Intrastat, and EC Sales Listings.

4. Track stock movement EU. When you transfer goods between EU warehouses, document them separately from Shopify sales. This matters for reporting Intra-EU stock movement and meeting Intrastat requirements.

5. Regular review. If you move stock to a new country, update Shopify right away (and register for a new VAT number).

Shopify can automate sales VAT calculations. But it will not file returns or track intra-EU stock transfers—you need those records for your VAT return preparation and extra country reporting.

Managing Intra-EU and Intra-UK Stock Movement

Answer-first: Every stock transfer—even without a sale—between EU countries or into/out of the UK requires documentation, Intrastat, and possibly EC Sales Listings.

Here’s how to manage Intra-EU Stock Movement:

• Always produce a stock movement record (an “internal invoice”) for each transfer.
• Log stock movements separately from Shopify sales invoices.
• File Intrastat returns monthly or quarterly, based on thresholds.
• Report cross-border B2B sales in the EC Sales Listing, as required.

Example: Moving 500 units from a German 3PL to a French Amazon FBA warehouse means you report that movement even if no sale occurred. The same applies for movements between UK and EU warehouses, with additional EORI documentation.

At 1stopVAT, we help clients develop simple checklists for every movement, so required filings are never missed. This is one of the biggest sources of error we see with Shopify sellers new to cross-border fulfillment.

Best Practices and Common Mistakes in VAT Compliance for Amazon FBA and Shopify

Answer-first: Staying on top of your VAT obligations means careful tracking, regular reviews, and getting country-specific advice.

Frequent errors include:

• Failing to register for VAT where stock is warehoused.
• Using only one VAT registration in Shopify, missing required rates elsewhere.
• Forgetting to report physical movements (not just sales) between EU warehouses.
• Relying solely on Shopify’s reports (which don’t show stock transfers).

How to avoid problems:

• Review all warehouse locations every quarter.
• Set calendar reminders for VAT, Intrastat, and EC Sales Listing filings.
• Use a tool or service—like 1stopVAT—that keeps your registrations and returns up to date.
• Ask a local VAT specialist before adding a new warehouse or country for stock.

We’ve seen businesses receive multi-country tax audits simply because one extra UK or EU warehouse was added and overlooked in VAT registration. Getting one-stop advice up front is always cheaper than dealing with a late penalty.

How to Stay Compliant with 1stopVAT for Amazon FBA and Shopify Sales

At 1stopVAT, our full-service approach means you’re not left guessing when you sell via Amazon FBA, Shopify, or both. Our clients have relied on us to:

• Manage VAT registration in each new EU or UK warehouse country
• Obtain EORI numbers for UK warehousing and cross-border trade
• File local VAT, Intrastat, and EC Sales Listings on time, every time
• Advice on VAT compliance from the first stock movement EU
• Integrate your Shopify records seamlessly for easy VAT returns

Our mission is to make VAT registration, compliance, and ongoing filing simple—even when you add a new 3PL location, or Shopify turns on a fresh market. Need to know if your plan is compliant? Our free consultation will give you a step-by-step roadmap tailored to your Amazon FBA and Shopify setup.

Final Remarks

The bottom line? Storing inventory in an EU country or the UK triggers VAT Registration, tax filings, and additional reporting, even if you only use Amazon FBA or a simple 3PL. Proper Shopify Tax Compliance and tracking of every stock movement in the EU are essential to avoid trouble and support business growth.

You do not have to do this alone. 1stopVAT helps sellers register, report, and manage compliance—so you never miss a filing or end up with mismatched VAT rates in Shopify. Ready to check your setup or need help with stock movement rules? Book a call with our team, and we’ll show you exactly what you need for your Amazon FBA and Shopify business.

Frequently Asked Questions