EU clarifies VAT on new €3 customs duty on low-value imports

The guidance follows the abolition of the long-standing customs duty exemption for consignments valued at €150 or less. It gives a major nudge for e-commerce sellers to use IOSS, which is backed by Import One-Stop Shop incentives on 1 July 2028. There are further measures in ViDA on securing IOSS.

€3 customs duty starts 1 July 2026

Under Council Regulation (EU) 2026/382, the EU will remove the €150 customs duty relief threshold from 1 July 2026.

As an interim measure running until 30 June 2028, a fixed customs duty of €3 per item will apply to distance sales of imported goods (DSIG) contained in consignments valued at no more than €150.

The duty becomes payable when the customs declaration for release into free circulation is accepted by customs authorities.

The Commission’s latest guidance focuses on a key question for importers and e-commerce sellers: does VAT also apply to the €3 customs duty?

IOSS users avoid VAT on the €3 duty

The most significant clarification concerns businesses using the Import One Stop Shop (IOSS).

Where IOSS is used:

• Import VAT remains exempt at the point of importation.
• VAT is instead charged at checkout when the customer places the order.
• The VAT is subsequently declared through the monthly IOSS return.
• No VAT is charged on the €3 customs duty.

The Commission explains that the €3 duty should not be included in the VAT taxable amount because the customs duty only arises when the goods are imported, not when the customer purchases the goods online.

This creates a small but notable advantage for IOSS users compared to other import models.

VAT applies to the €3 duty under Special Arrangements

Different treatment applies where businesses rely on the Special Arrangements regime instead of IOSS.

Under this simplification:

• Import VAT remains due.
• Postal operators and carriers collect the VAT from customers.
• The customer remains legally liable for the import VAT.

Because VAT is charged at importation, the €3 customs duty must be included within the VAT taxable amount.

This means customers effectively pay VAT on both the imported goods and the €3 customs duty.

Where goods are returned, the VAT relating to the customs duty should also be refunded.

Standard import procedures follow the same approach

The Commission confirms identical treatment for imports processed under normal customs procedures.

Where neither IOSS nor the Special Arrangements are used:

• Import VAT is due under standard import rules.
• The €3 customs duty forms part of the VAT taxable amount.
• VAT is therefore charged on the customs duty itself.
• Any subsequent refund should include VAT paid on the €3 duty.

Future EU handling fee will be outside VAT

The guidance also addresses the planned €2 EU Customs Union handling fee expected to be introduced as part of the wider EU Customs Reform package.

This fee is not expected before November 2026.

Unlike the €3 customs duty, the Commission confirms that the handling fee will be treated as consideration for a public authority service performed by customs authorities.

As a result:

• The handling fee will be outside the scope of VAT.
• No VAT will be charged on the fee.
• The fee will not form part of the VAT taxable amount at importation.

This distinction means businesses may face both a customs duty that attracts VAT and a handling fee that does not.

What this means for e-commerce sellers

The Commission’s clarification reinforces another commercial advantage of the IOSS regime.

Businesses using IOSS will not only continue to benefit from a smoother customer experience and faster customs clearance, but they will also avoid VAT being charged on the new €3 customs duty.

For marketplaces, online retailers and logistics providers handling large volumes of low-value imports, the guidance provides important certainty ahead of the customs reforms taking effect on 1 July 2026.