Portugal airports return to 100% biometric checks: Who is affected?

Portugal has restored biometric data collection at airport border controls to 100% from 6 September. The measure is part of the European Union's Entry/Exit System (EES) and mainly concerns certain third-country nationals travelling to the Schengen area for short stays. However, several groups — including many people who hold a valid Portuguese residence permit — are exempt from EES registration.

Prime Minister Luís Montenegro said during a visit to Lisbon's Humberto Delgado Airport on 27 August that returning biometric data collection to 100% from 6 September could place additional pressure on border-control operations.

The measure forms part of the EU's Entry/Exit System, an electronic border-management system designed to replace manual passport stamping with digital entry and exit records. Depending on the traveller's status, the system can record travel-document details, a facial image and fingerprints.

Portugal began the phased rollout of EES in October 2025, and the system became fully operational at air and sea border crossing points on 10 April 2026.

What changed on 6 September?

EES did not start in Portugal on 6 September. It was already in operation. During periods of heavy passenger pressure, Portugal had been able to use temporary measures allowed under the European framework to reduce or suspend biometric data collection for limited periods.

The change on 6 September was therefore the return to full biometric collection at 100%. The Portuguese government has acknowledged that this can create additional pressure at major airports such as Lisbon, Porto and Faro.

Who is covered by EES?

EES mainly applies to third-country nationals travelling to the Schengen area for short stays of up to 90 days in any 180-day period, whether they are visa-required or visa-exempt.

For a visa-exempt traveller, the first EES registration may include a facial image and four fingerprints. For travellers holding a short-stay Schengen visa, fingerprints may already have been collected during the visa process, so the EES procedure can rely primarily on the facial image. Children under 12 are not fingerprinted under EES.

Important for Portuguese residence permit holders

One of the most important points for foreign residents in Portugal is that EES does not apply to everyone. According to the European Commission, third-country nationals who hold a valid long-stay visa or residence permit issued by a country using EES are exempt from EES registration.

This means that a person travelling with a valid Portuguese residence permit is not in the same position as a short-stay visitor entering Portugal as a tourist. EU citizens, as well as citizens of Iceland, Liechtenstein, Norway and Switzerland, are also not registered in EES.

Will passports still be stamped?

One of the main purposes of EES is to replace traditional manual passport stamps with electronic entry and exit records. The system records when a traveller enters and leaves the Schengen area and helps determine whether the permitted 90-day stay within a 180-day period has been exceeded.

Will there be longer queues at airports?

This has been one of the main concerns since EES began to be introduced in Portugal. The Portuguese government has acknowledged that significant waiting times were recorded at Lisbon Airport during the early phase of implementation.

Authorities say that technology upgrades, additional staff and closer coordination between services have improved processing times. Before the return to 100% biometric collection, Portugal's National Unit for Foreigners and Borders (UNEF) carried out stress tests at airports.

According to UNEF data reported by Renascença, 90% of passengers at Lisbon Airport waited less than 15 minutes on departure and less than 20 minutes on arrival during the tests. The figures do not mean that longer queues are impossible during peak periods.

What should travellers to Portugal do?

Non-EU travellers visiting Portugal for a short stay should allow extra time for border formalities, especially if they are completing an EES registration for the first time.

Foreign residents of Portugal who hold a valid residence permit or long-stay visa should continue to travel with their valid passport and residence documentation and be aware that their EES status is different from that of a short-stay visitor.

EES is not a visa or a residence permit. It is an electronic border-control system that records short-stay entries and exits at the EU's external borders.

Reviewed Sources

Government of Portugal — Prime Minister Luís Montenegro's airport border-control statement of 27 August 2026.

Sistema de Segurança Interna — Information on the scope of EES, biometric data and implementation in Portugal.

European Commission — EES exemptions, including the position of residence-permit and long-stay visa holders.

Renascença — Anabela Góis — 4 September 2026; UNEF stress tests and airport waiting-time data.

RTP / Lusa — Reporting on Portugal's return to 100% biometric data collection and the government's statements.