Shopify IOSS Apps 2026: Register, Collect, and File EU VAT

---

If you sell to EU consumers, IOSS (Import One-Stop Shop) is the mechanism that lets you collect VAT at checkout instead of making customers pay at the door. Shopify apps make it manageable — but there's one thing no IOSS app will tell you: it never covers customs duty.

What IOSS apps actually do

Function	What it does
Registration	File your IOSS registration with the EU (or help you do it)
VAT collection	Add correct EU VAT rates at checkout per destination country
Filing	Prepare and submit your quarterly IOSS VAT returns
Compliance	Track thresholds and flag countries with special rates

What IOSS apps do NOT do

• Collect the €3 customs duty (€5 from November 1, 2026) — that's a customs charge, not VAT
• Handle HS codes or customs classification
• Fix declaration-line overcharges — multi-line orders still get charged €3–€5 per line regardless of your IOSS status

This gap is the #1 confusion in 2026: sellers assume IOSS = "all EU charges handled." It isn't. IOSS is VAT-only by design.

The IOSS + duty math

A €60 order to Germany, 2 declaration lines:

• VAT via IOSS: ~€12 (20% rate)
• Customs duty: 2 × €3 = €6 (2 × €5 = €10 from November 1) — not covered by IOSS

IOSS fixes the VAT side. The duty still exists, still charges per line, and still surprises customers unless you've handled it separately.

How to choose an IOSS app

1. Check EU coverage — does it handle all 27 member states' rates? 2. Check filing support — quarterly IOSS returns are the real workload 3. Check price — percentage-of-sales pricing vs. flat fee 4. Understand the duty gap — whatever you pick, you still need customs-side visibility

The missing piece

Even with perfect IOSS setup, you still can't see the €3/€5 duty in Shopify — so you don't know if multi-line orders are overcharging you, or if your prices cover the real cost.

That's a separate problem from VAT, and it needs a separate tool: an audit that reads your orders and flags customs-side exposure.