Missing VAT on your Shopify invoices: causes and fixes

You generate an invoice from your Shopify store and… no VAT. Missing line, €0 amount, or a net total equal to the gross. Before blaming your invoicing app, know that in almost every case, the cause lies in Shopify’s tax settings. Let’s review them.

Understanding where invoice VAT comes from

An invoicing app like FacturX does not “compute” VAT itself: it faithfully reproduces the taxes Shopify calculated at order time, rate by rate. If Shopify applied no tax to the order, the invoice cannot display any. That is the correct behavior: an invoice must reflect the real transaction.

So if VAT is missing, the order itself was placed without VAT. Here is why that happens.

Cause #1: VAT collection is not enabled for France

In the Shopify admin, open Settings → Taxes and duties. Check that France (and the European Union if relevant) appears among the regions where you collect tax, with your intra-community VAT number filled in.

Without this, Shopify charges everything at 0% — and so do your invoices.

Cause #2: products are marked as non-taxable

Every product has a “Charge tax on this product” checkbox. If it is unchecked (a frequent side effect of CSV imports), the product sells tax-free.

Check the product page, Pricing section. To fix in bulk, use Shopify’s bulk editor.

Cause #3: the customer is tax-exempt

A customer can be marked “tax exempt” on their customer profile (common after tests, or for intra-EU B2B customers under reverse charge). That customer’s orders then go out without VAT — and sometimes that is intended: an intra-EU B2B sale with a valid VAT number is legitimately at 0%, with the reverse-charge mention.

Cause #4: you are under the French VAT franchise

If your business benefits from the franchise en base (article 293 B of the French tax code), you do not charge VAT — that is normal. But your invoice must then carry the mandatory mention:

“TVA non applicable, art. 293 B du CGI”

In FacturX, add this mention to your template’s footer (Configuration → Template). And if you exceed the franchise thresholds during the year, remember to enable collection in Shopify from the very first day you become liable.

Cause #5: tax-inclusive vs tax-exclusive prices misconfigured

In Settings → Taxes and duties, the “All prices include tax” option changes everything:

• enabled: your catalog prices are gross, Shopify extracts VAT from the price;
• disabled: your prices are net, VAT is added at checkout.

A mismatch here does not make VAT disappear, but produces surprising amounts (VAT “included” the customer did not expect, totals that look wrong). Make sure the setting matches what you actually display.

How to check everything is back in order

1. Place a test order with a taxable product and a French shipping address;
2. Open the order in the admin: the “Taxes” line must show VAT (20%, 10%, 5.5%…);
3. Generate the invoice: FacturX displays the breakdown per rate (net basis, rate, amount) in the totals table, and writes it into the Factur-X XML.

The bottom line

An invoice without VAT is not always an error — the VAT franchise, exports and intra-EU reverse charge are legitimate cases that simply require the right legal mention. For every other case, the fix lives in Shopify’s tax settings, never in the invoicing app.

Need invoices with a clean VAT breakdown per rate? Install FacturX for free: per-rate breakdown, customizable mentions and Factur-X compliance included.