EU Biometric Border Checks Causing Long Queues at Portuguese Airports

The European Union’s Entry-Exit System (EES) became fully operational at all Portuguese border crossing points on 10 April 2026, and the results have been disruptive. Travellers arriving from outside the EU are reporting queue times exceeding one hour at Lisbon Humberto Delgado Airport, Porto Sá Carneiro Airport, Faro Airport, and Funchal Airport in Madeira.

The EES replaces the traditional passport stamp with a digital record: fingerprints and a facial scan, logged alongside entry and exit dates. The system applies to all non-EU, non-EEA travellers making short stays of up to 90 days within any 180-day window across the Schengen Area. UK nationals are included following Brexit. EU, EEA, and Swiss passport holders pass through as normal and are unaffected.

The disruption reached a peak on 12 May, when approximately 237 flights were delayed and 6 cancelled across Lisbon and Porto. Lisbon recorded 185 delays and 3 cancellations; Porto logged 52 delays and a further 3 cancellations. Ryanair has publicly called on the Portuguese government to suspend EES enforcement until border infrastructure can handle peak summer volumes.

This is not the first time Portugal has struggled with the rollout. Earlier in the implementation, Lisbon Airport temporarily suspended the system when arrival queues stretched to seven hours, disrupting connections and leaving passengers stranded overnight. The current situation is less severe but still falling short of the capacity needed as the summer travel season begins.

What to do before your trip

Add 90 minutes to your airport buffer. If you hold a non-EU passport, build in at least 90 extra minutes beyond your usual pre-flight window when arriving at Lisbon, Porto, Faro, or Funchal. Queues are longest on arrival, not departure.

Protect connecting flights. If you are transiting through a Portuguese airport, we recommend a minimum three-hour connection time for international-to-international journeys. Shorter layovers carry real risk of being missed.

Check your carrier’s updates. Airlines are actively monitoring the situation. Sign up for flight status alerts and check your airline app in the 48 hours before travel.

EU passport holders are unaffected. If you hold a passport from an EU, EEA, or Swiss member state, standard border lanes apply and you will not encounter EES queues.

For a broader overview of safety and practical matters, our Portugal safety guide covers everything from emergency numbers to petty crime. Arriving into the south? Our Algarve guide covers transport from Faro Airport. Arriving into the capital or Porto, our guides to Lisbon and Porto include airport transfer options for both cities.