Two charges land on a non-EU import, and they're calculated over different bases. That's where the numbers usually go wrong. The short version: duty is calculated over the goods plus transport to the border; VAT is then calculated over that plus the duty plus onward transport. Nexport Logistics gets the base right on your declaration in the Nexportal portal. This sits next to Reverse Charge Vat and the commercial invoice that drives it.
The customs value (douanewaarde)
The customs value is the basis for the import duty. As a rule it's the transaction value, the price actually paid for the goods, plus the transport and insurance costs up to the point of entry into the EU (the EU border or port). That's broadly a CIF-type value. The import-duty percentage (set by the HS/TARIC code and the goods' origin) is applied to this customs value.
The import-VAT base
The import VAT is calculated over a wider base: the customs value + the import duty + ancillary costs (transport and insurance) up to the place of destination within the EU. So onward transport from the border to the delivery address inside the EU is in the VAT base, even though it isn't in the duty base.
It follows that the transport service into the EU is itself 0% VAT: that transport is already taxed inside the import-VAT base, and taxing the carrier's invoice too would be double taxation. (That's the link to the 0% import-transport rule.)
A simple worked example
- Goods (per the commercial invoice): €10,000
- Sea freight + insurance to Rotterdam: €1,000
- → Customs value = €11,000
- Import duty, say 4% of €11,000 = €440
- Onward transport Rotterdam → your door: €300
- → Import-VAT base = €11,000 + €440 + €300 = €11,740
- Import VAT at 21% = €2,465.40
With an Article 23 licence that VAT isn't paid at the border but deferred to your periodic VAT return, so it doesn't tie up your cash.
(Rates and the exact treatment depend on the goods and the situation; always confirm on the official source.)
Preferential origin: pay less or zero duty (EUR.1, A.TR)
The duty rate isn't always the standard third-country one. If the goods have preferential origin under an EU trade agreement, a EUR.1 certificate (a movement certificate, the preferential proof of origin; the full mechanism, the EUR 6,000 invoice-declaration threshold and the approved-exporter licence are on Preferential Origin) can get you a reduced or zero duty rate. It applies to imports from countries the EU has a preferential agreement with; examples include Switzerland, Norway, Egypt and Morocco, among many others. Several newer agreements (e.g. Japan, Canada) instead work with a self-certified statement on origin / origin declaration by the exporter rather than a EUR.1, and each agreement has its own proof rules (South Korea uses an approved-exporter origin declaration; Vietnam still issues EUR.1 for imports into the EU), so always check the agreement that applies to your origin country.
An A.TR certificate is different: it is specific to Türkiye and certifies that goods are in free circulation within the EU–Türkiye customs union, so they move without import duty. It is not an origin certificate; it's about customs-union status, and it works in both directions (EU→TR and TR→EU). Agricultural and coal/steel products fall outside the customs union and use EUR.1 instead. The duty rule and the certificate of origin decide whether you qualify; the certificate is issued/validated at origin and presented with your import declaration.
How Nexport Logistics gets it right
Nexport Logistics works as a freight forwarder under the FENEX conditions, with its own customs declarants. We build the customs value correctly, apply the right duty rate for your HS/TARIC code, get the import-VAT base right, and arrange the Article 23 deferment so import VAT doesn't tie up your cash flow, all in the Nexportal portal. Want your landed cost calculated? Email info@nexportlogistics.nl.
Official sources: Belastingdienst — calculating VAT on imports · EU customs tariff (tarief.douane.nl). Related: Customs · Reverse Charge Vat · Shipping Documents · Importing Into The Netherlands