Portugal’s two busiest holiday gateways, Lisbon and Faro, are grappling with growing disruption linked to the European Union’s new biometric border controls, raising concerns about hours-long queues just as airlines and hotels prepare for the crucial 2026 summer season. The Entry Exit System, or EES, launched across the Schengen area in October 2025, is intended to tighten border security and replace manual passport stamping for non-EU nationals. In practice, it has exposed serious capacity constraints at Portugal’s airports, prompting an unprecedented three-month suspension of the system at Lisbon and sparking fears that similar pressure at Faro could hit Algarve tourism at its peak.
What Is EES and Why It Is Hitting Portugal So Hard
The EU’s Entry Exit System is a large-scale biometric database designed to record the crossings of all non-EU, non-Schengen nationals entering or leaving the bloc. Instead of a simple passport stamp, travelers from countries such as the United States, United Kingdom, Canada, Brazil and dozens of others must now complete a digital registration that captures their facial image, fingerprints and passport details on first entry, and then verifies their identity on subsequent trips. Authorities argue that EES will make it easier to spot overstays and identity fraud and to enforce the widely known 90 days in 180 rule for short stays in the Schengen zone.
The challenge is that this first registration can take several minutes per passenger, especially when done at manual booths rather than automated kiosks. Airports across Europe have warned that border processing times for non-EU travelers have increased by as much as 70 percent since the rollout began, with peak-period waits of up to three hours already reported. In Portugal, these pressures collide with particularly tight infrastructure at Humberto Delgado Airport in Lisbon, which handled more than 36 million passengers in 2025 despite being designed for around 22 million, and more than 10 million at Faro, a gateway heavily skewed to seasonal leisure traffic.
Lisbon’s squeeze is especially acute because it serves as both an origin and hub for long-haul markets outside Schengen, feeding TAP Air Portugal’s network and a dense schedule of flights from North America, Brazil and Africa. A high share of arriving passengers are therefore subject to EES controls, many of them landing within short arrival banks that quickly flood the border area. With limited physical space to expand queues or add equipment, even modest slowdowns have translated into dramatic bottlenecks at immigration.
How EES Has Already Triggered Chaos at Lisbon Airport
When Portugal activated EES on October 12, 2025, border authorities initially described the transition as a success. Within days, however, social media began to fill with images of packed corridors at Lisbon’s Terminal 1, with non-EU passengers reporting waits of 90 minutes or more at passport control. Police officials acknowledged that some days were “critical,” with heavy long-haul arrival waves exposing just how much longer each individual check was taking under the new biometric process.
By December, the situation had deteriorated further. Technical glitches in border control systems, combined with the added complexity of EES, led to waiting times of three hours and more at Lisbon, according to the Public Security Police. Airlines and airport staff reported travelers missing connections and spending large portions of their arrival day inching forward in crowded lines. The government responded by deploying an emergency task force and surging additional officers to man every available booth, while ANA Aeroportos de Portugal, the airport operator, began distributing water and snacks in the queues as a stopgap measure.
The climax came over the busy 2025–2026 holiday period, when reports emerged of passengers at Lisbon waiting as long as seven hours to clear border control. Faced with what officials described as “serious deficiencies” in arrivals infrastructure and staffing, the Ministry of Internal Administration took the extraordinary step of suspending EES at Lisbon in early January 2026 for a three-month period. During this pause, border checks for non-EU nationals have reverted largely to pre-EES procedures, easing congestion but leaving Portugal temporarily outside the full biometric regime that the rest of the Schengen area is moving towards.
Faro’s Rising Risk: Algarve Tourism in the Firing Line
While Lisbon has grabbed most headlines, the implications for Faro Airport and the wider Algarve are becoming a growing concern for the travel industry. Faro handled more than 10 million passengers in 2025, a figure that has steadily climbed in the post-pandemic rebound. Unlike Lisbon, where traffic is spread relatively evenly across the calendar, Faro’s demand is highly concentrated in the spring and summer months, amplified by a heavy reliance on British, Irish and other non-EU holidaymakers who are directly affected by EES.
During July and August, waves of leisure flights from regional airports across the United Kingdom, Scandinavia and central Europe arrive within tight time windows, creating intense pressure on both arrivals and departures facilities. Industry bodies and tour operators warn that if EES registrations are fully enforced without additional staff and technology, queues of four to five hours at passport control in Faro are not unrealistic during peak days. For families landing with children and luggage in the Algarve heat, or facing tight turnaround times for package transfers to coastal resorts, such delays would be more than a nuisance. They risk undermining the region’s hard-won reputation for easy, stress-free access.
Local tourism leaders in the Algarve have already begun pressing the central government and ANA for clarity on Faro’s readiness. They are calling for extra passport booths, an expansion of automated e-gates for eligible travelers and clear contingency plans if queues spike. Hoteliers and villa operators, many of whom are counting on a strong British and northern European market this summer, worry that viral images of snarled lines at Faro could deter last-minute bookings or push visitors toward competing destinations in Spain and beyond.
Government and Airport Responses So Far
In response to the mounting criticism, Portuguese authorities have set out a series of measures aimed at stabilizing border operations ahead of the summer. The emergency task force created in late 2025 has been tasked with coordinating between the Public Security Police, the Internal Security System, the Ministry of Internal Administration and ANA. Its brief ranges from immediate crisis management to medium-term capacity improvements at Lisbon and Faro.
At Lisbon, officials report that additional officers have been trained and assigned to border posts, with all available booths open during busy periods. Technical teams are working to resolve software issues that plagued the early EES rollout and to improve the reliability of the RAPID e-gate system used by EU and some third-country nationals. Internal monitoring suggests that average wait times for non-EU arrivals have already come down from the worst peaks, although they still frequently exceed one hour on busy days, even with EES currently suspended.
For Faro, authorities have been more guarded in their public messaging, but planning documents point to a similar strategy. These include reinforcing staffing levels during peak arrival waves, reconfiguring queuing space in the arrivals hall, and deploying additional self-service kiosks where EES registration can be completed before travelers reach the officer booths. The government has also welcomed new flexibilities granted by the European Commission, which allow member states to temporarily limit or pause EES checks at specific border points during exceptional peaks, as long as core security requirements are maintained.
Will EES Be Fully Back by the Summer Peak?
A key question for anyone planning a trip to Portugal in 2026 is what EES will actually look like by the time the summer season begins. The system formally launched in October 2025, but its rollout is phased, with a requirement that member states have the technology in place at all external border points by April 10, 2026. At the same time, Brussels has given countries considerable leeway in how quickly they move from a partial to full registration rate of third-country travelers, especially where infrastructure is strained.
In practice, that means travelers can expect a patchwork experience, at least through the summer. At some airports in Europe, including certain Portuguese terminals, EES kiosks are already in broad use and a significant share of non-EU arrivals must register biometrics. At others, authorities are using the available flexibilities to cap the percentage of travelers processed under EES at any given time or to suspend the system temporarily when waiting times reach unacceptable levels. Industry associations have urged the Commission to formally endorse such seasonal pauses to avoid what they describe as potential five to six hour queues at peak.
For Lisbon, the current three-month suspension, running through early April 2026, is explicitly framed as a window to fix the worst bottlenecks before EES is reinstated. Whether that pause is extended into the heart of the summer travel season will depend on the outcome of technical upgrades, staffing reinforcements and capacity tweaks on the ground. Faro, which has not suspended EES in the same way, is likely to see a more incremental ramp-up, with authorities adjusting registration rates and controls in real time as the summer schedule builds.
What Non-EU Travelers Should Expect at Lisbon and Faro
For visitors from the United States, United Kingdom and other non-EU countries, the main impact of EES is at the point of entry into Portugal and the Schengen zone. On your first trip after the system is fully applied, you must undergo full biometric registration. This typically involves scanning your passport at a kiosk, having your fingerprints taken and your photograph captured, and then presenting the resulting token to a border officer or dedicated e-gate. On later trips, the process should be faster, as your data is already stored, but your passport will still be checked against the database.
At Lisbon, travelers should be prepared for mixed conditions in 2026. While EES is paused, you may find that checks feel closer to pre-2025 norms, albeit with occasional surges when several long-haul flights arrive together. Once the system is switched back on, particularly if this coincides with the late spring or early summer rush, expect significantly longer queues for non-EU arrivals. Passengers connecting onward to domestic or Schengen flights should allow generous minimum connection times and consider booking through tickets on a single airline or alliance so they are protected if delays at border control cause missed connections.
At Faro, even if official waiting times remain shorter than Lisbon’s worst days, leisure travelers should not underestimate the potential for disruption. The combination of tight arrival peaks and high shares of EES-eligible passengers means that queues can build quickly. Families arriving on morning or late-night banked services should factor in the possibility of a one to two hour wait at passport control, with longer delays a real risk on the busiest Saturdays of July and August. On departure, non-EU passengers can also face secondary queues if outbound checks are reinforced, so allow ample time to reach your gate.
Practical Strategies to Reduce the Pain
While individual travelers cannot change the structure of border systems, they can take practical steps to reduce the impact of EES-related congestion on their trip. The first is to build in time. If you are landing at Lisbon or Faro on a separate ticket from your onward connection, avoid tight layovers and consider staying overnight if the next available flight leaves within only a few hours of arrival. For direct holiday trips to the Algarve or Lisbon city, plan ground transfers or hotel check-ins with enough flexibility to absorb an extended wait at immigration without triggering cascading stress.
When choosing flights, off-peak timings can make a difference. Early afternoon or late evening arrivals may face less crowding than traditional morning bank periods, when transatlantic services from North America often coincide with holiday flights from the United Kingdom and northern Europe. Travelers with flexibility might also look at shoulder-season dates in May, early June or September, when airports are busy but not yet at their summer saturation point and when authorities may have more latitude to manage EES registration rates smoothly.
Once at the airport, simple habits help. Use restrooms before joining the border queue, carry a refillable water bottle and a small snack, and keep essential medications in your hand baggage. Have your passport ready and remove hats or sunglasses in advance to speed up biometric capture. Families should gather children and belongings before reaching the front of the line so that the actual processing time at the booth is as efficient as possible. Small efficiencies matter when multiplied by thousands of passengers.
What This Means for Portugal’s Tourism Image
The EES disruption arrives at a delicate moment for Portugal’s tourism economy. After a record-breaking 2025, with more than 72 million passengers passing through the country’s airports, Lisbon, Porto and Faro are all pushing at the limits of their infrastructure. For the Algarve and Lisbon city break markets in particular, ease of access has been one of the country’s most important competitive advantages, helping it stand out among Mediterranean rivals with more congested gateways or complex arrival procedures.
Extended queues at border control threaten to chip away at that advantage. Tour operators and hotel groups worry that if scenes of seven-hour waits or chaotic passport halls gain traction internationally, potential visitors could look elsewhere, especially for shorter stays where every hour counts. The travel industry is pressing the government to treat border capacity as core tourism infrastructure, on a par with runways and terminals, and to invest accordingly in staffing, technology and, where possible, physical expansion.
For now, Portugal remains firmly on the wish lists of travelers around the world, and demand for summer 2026 is strong. The question is whether the country can align its border systems with that demand quickly enough to avoid a repeat of the 2025 holiday chaos. For would-be visitors, the message is not to avoid Lisbon or the Algarve, but to come informed, plan conservatively and keep a close eye on developments as the summer approaches. With realistic expectations and a bit of buffer time, you can still enjoy Portugal’s beaches, cities and wine country, even as its airports navigate the turbulence of Europe’s new biometric era.