Holidaymakers heading home from Spain are being warned to brace for long queues and potential missed flights as the European Union’s new Entry/Exit System continues to cause disruption at passport control, with Malaga Costa del Sol Airport emerging as one of the worst hotspots.

Low cost carrier Ryanair has issued targeted alerts to customers flying from Spanish airports, urging them to arrive significantly earlier than usual and proceed straight to security and border checks amid reports of two hour waits and mounting frustration at the terminals.

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Ryanair tells passengers to arrive earlier amid mounting complaints

Ryanair has begun emailing customers flying from Spain, particularly from busy leisure gateways such as Malaga, warning that “longer queues” are being recorded at passport control due to the roll out of the EU’s Entry/Exit System.

The airline is advising passengers on flights to non Schengen destinations, including the United Kingdom and Ireland, to arrive at the airport at least three hours before departure and to go directly to security and passport control after dropping off luggage in order to avoid being caught in lengthy bottlenecks.

The carrier’s warning follows a surge of complaints on social media and to local media outlets from travelers who say they queued for well over an hour, and in some cases up to two hours, to clear border checks at Malaga in recent weeks.

Some report that by the time they reached their departure gate, their flight had already closed, forcing them to rebook and arrange unexpected overnight stays on the Costa del Sol at the height of the festive travel period.

Ryanair has publicly criticized what it sees as inadequate planning and resourcing by Spanish authorities, arguing that the new system has been introduced without sufficient staffing or technical support.

While the airline cannot control what happens at passport control, the warning is intended to protect its operations and reduce the number of passengers arriving late to the gate.

Other carriers operating out of Malaga are also understood to be quietly advising travelers to factor in extra time for border checks.

Malaga becomes a symbol of EES teething problems

Malaga Costa del Sol Airport has repeatedly been singled out by passengers as one of the airports worst affected by the Entry/Exit System’s early implementation.

Since late October, when Spain began adapting some of its major airports to the new EU border regime, regular flyers have reported that queues at passport control, which previously took 15 to 30 minutes to clear, can now stretch well beyond an hour at peak times.

Local newspapers have published images of snaking lines reaching back towards duty free and even into public areas of Terminal 3.

Accounts from travelers describe scenes of “total chaos,” with only a handful of staffed passport booths open and rows of EES biometric kiosks either inactive, taped off or flashing error messages. Some non EU passengers say they queued first for the machines, only to be sent back into a manual line when the technology failed, effectively doubling their wait.

Others recount queues rising up staircases inside the departures area and warn that a sudden surge of impatient passengers could create safety issues in already congested corridors.

Airport operator Aena and Spain’s Interior Ministry have sought to downplay the disruption, describing the situation as part of a normal adjustment process during a transition period in which both manual and electronic checks are running side by side.

Officially, the machines at Malaga are being used in limited trial windows, with manual stamping still available at staffed booths.

Yet the volume and consistency of passenger complaints suggest that for many travelers, particularly those heading back to the UK and Ireland, Malaga has become synonymous with long, unpredictable waits at the border.

How the EU’s new Entry/Exit System works

The Entry/Exit System is a flagship EU border security project designed to replace traditional manual passport stamping for non EU nationals entering and leaving the Schengen Area.

Instead of a quick ink stamp, travelers from third countries such as the United Kingdom, Ireland and the United States now need to undergo biometric registration the first time they cross an external Schengen border after full implementation.

This typically involves scanning a passport, providing fingerprints and having a facial image captured at an automated kiosk or by a border officer.

The system records the time and place of entry and exit for each traveler and automatically calculates how long they have stayed in the Schengen Area. Its primary aim is to strengthen security, combat identity fraud and ensure enforcement of the well known 90 day rule that limits short stays by non EU visitors to 90 days in any rolling 180 day period.

In theory, once a traveler has been registered and their biometric data stored, subsequent crossings should be quicker, with the system verifying their identity and stay history against the database in a matter of seconds.

In practice, however, the early months of the rollout have exposed significant weaknesses. At airports where passenger numbers remain high, every additional step in the border process, such as fingerprint capture or troubleshooting a faulty kiosk, adds seconds or minutes to each transaction.

When multiplied across planeloads of passengers arriving within tight time windows, this has led to long lines and missed connections, particularly where staffing levels remain fixed to pre EES assumptions and not enough officers are available to intervene when machines malfunction.

Technical glitches, staffing shortages and confusing signage

Reports from Malaga and other Spanish airports indicate that the disruption is not solely due to the intrinsic complexity of the new technology. Passengers and travel industry observers point to a combination of factors that have turned what should have been manageable delays into major bottlenecks.

Among the most commonly cited problems are biometric kiosks going offline without warning, fingerprint readers failing to capture prints from older travelers, and language or interface issues that leave some users unsure how to complete the process.

When kiosks fail, lines are often redirected to a limited number of staffed booths, where officers must revert to manual passport checks and, in some cases, manually input data that was supposed to be captured automatically.

This slows throughput even further. Complaints also highlight poor signage in some terminals, with non EU travelers unsure whether to join the EES queue, the traditional passport line, or an EU and Schengen residents lane.

At Malaga, witnesses report that queues have become mixed, with EU citizens and Spanish residents sometimes lining up alongside tourists subject to biometric registration, further complicating traffic flow.

Staffing levels at border control remain a sensitive topic. Police unions and aviation industry groups have warned that without a significant increase in the number of trained officers, the system will struggle to cope during peak travel seasons.

Over the Christmas period, Malaga recorded some of its busiest days of the year, coinciding with an increase in EES use. While extra officers have been deployed at some airports in other EU countries on a temporary basis, travelers passing through Malaga and other Spanish hubs say they frequently see only two or three booths open at times when multiple flights from the UK and Ireland are disembarking simultaneously.

British and Irish travelers at the sharp end

For British and Irish holidaymakers, the EES rollout has brought into sharp focus the post Brexit reality of travel to mainland Europe. Citizens of both countries are treated as third country nationals at Schengen borders, meaning they are fully subject to the new biometric checks.

As a result, popular sun destinations along Spain’s Mediterranean coast are now seeing longer passport control queues for flights bound for the UK and Ireland, especially during busy return days at the end of school holidays and festive breaks.

Many of those caught up in the delays at Malaga over the past two months have been families returning from week long winter sun breaks or city trips to Andalusia, often with children in tow.

Some have missed flights entirely after getting stuck in queues, despite arriving at the airport with what they believed to be sufficient time to spare.

Social media posts from late December describe passengers sprinting through terminals after finally clearing passport control, only to watch boarding gates close in front of them.

The confusion has been particularly acute for British citizens who are legal residents in Spain and hold residence cards. Conflicting messages from different Spanish authorities about which lane they should use have led some to join the EES queue, while others have been turned away and sent to staffed booths.

Recent guidance from national police and the Interior Ministry now indicates that residents with valid documentation should avoid EES kiosks and instead present their passport and residence card directly to an officer.

However, not all passengers are aware of the updated advice, and implementation on the ground has not always been consistent.

Authorities under pressure to stabilize the system

Spanish authorities insist that the current turbulence is temporary and that performance will improve as staff gain experience, software bugs are ironed out and travelers become more familiar with the process.

The Interior Ministry has emphasized that the EES is still in a trial or transition mode at several airports, including Malaga, and that manual checks remain available while the system is phased in over a six month period.

Officials argue that the benefits in terms of security and more accurate tracking of overstays will outweigh the early inconvenience.

Nonetheless, with the Christmas peak barely over and the busy Easter and summer seasons already on the horizon, pressure is mounting on both the Spanish government and the EU to show that the system can operate smoothly under heavy load.

Local tourism leaders along the Costa del Sol worry that persistent reports of chaotic queues and missed flights could deter repeat visitors or push British and Irish travelers to consider alternative destinations.

Airlines, for their part, are keen to ensure that passengers do not blame carriers for disruption at border control that lies outside their direct control.

Industry groups are calling for a combination of measures, including additional staffing at peak times, clearer airport signage separating EES users from other passengers, extended communication campaigns to explain the new system and better contingency planning when kiosks fail.

There is also growing discussion about whether certain categories of travelers, such as long term residents with biometric residence cards, should be exempted from repeated EES registration in order to reduce pressure on the system.

Advice for travelers using Malaga and other Spanish airports

In the short term, passengers flying from Malaga and other Spanish airports affected by the Entry/Exit System are being urged to build generous buffers into their travel plans.

Ryanair’s advice to arrive at least three hours before departure for non Schengen flights is increasingly being echoed by frequent flyers, who recommend treating passport control as a potential bottleneck rather than an afterthought.

Travelers are also being encouraged to head straight for security and border checks after check in instead of lingering landside in shops, bars or restaurants.

Non EU nationals should ensure they have all required documents ready before reaching passport control, including passports, boarding passes and any proof of onward travel or accommodation that might be requested.

Those undergoing biometric registration for the first time should be prepared to follow instructions at the kiosks carefully and allow extra time for the process.

Families with children, older travelers and those with reduced mobility may wish to inquire in advance about assistance services offered by airports or airlines to help mitigate the impact of long waits.

British residents in Spain who hold a valid residence card are advised to pay close attention to the latest guidance from Spanish authorities at the time of travel and to seek out staffed booths rather than EES lanes where instructed. They should carry both their passport and residence document and be ready to explain their status to border officers if necessary.

Above all, passengers are urged to monitor communications from their airline in the days leading up to departure, as carriers like Ryanair continue to update their advice in response to evolving conditions at the airports.

FAQ

Q1. What exactly is the EU Entry/Exit System and why is it causing delays in Spain?
The Entry/Exit System is a new EU wide database that records the entry and exit of non EU nationals at external Schengen borders using passport scans and biometric data. At Spanish airports such as Malaga, the extra steps involved in biometric registration, combined with technical glitches and limited staffing, have lengthened the time it takes border officers to process each traveler, resulting in queues and missed flights during busy periods.

Q2. Why has Ryanair issued a travel warning for flights from Malaga and other Spanish airports?
Ryanair has sent warning emails after receiving reports of long passport control queues linked to the Entry/Exit System. The airline is urging passengers to arrive much earlier than usual and to go straight to security and passport checks to reduce the risk of reaching the boarding gate too late. While the carrier is not responsible for border control operations, it is trying to minimize disruption to its flight schedule and help customers avoid delays.

Q3. Which passengers are most affected by the new system at Malaga?
The travelers most affected are non EU nationals, particularly those returning to the United Kingdom, Ireland and other non Schengen destinations from Spanish holiday spots. These passengers are subject to biometric registration under the Entry/Exit System and often arrive in large numbers on closely spaced flights, which can quickly overwhelm passport control if staffing and equipment are not sufficient.

Q4. How long are current waits at passport control in Malaga?
Wait times vary by day and time, but recent accounts from passengers and local media describe queues lasting more than an hour on busy days and, in some extreme cases, approaching two hours. At quieter times, processing can still take around 15 to 30 minutes, but travelers are being warned that conditions can deteriorate rapidly when several flights arrive or depart in quick succession.

Q5. What can I do to reduce my chances of missing a flight from Malaga?
The most important step is to arrive at the airport well in advance of your scheduled departure, ideally at least three hours before a non Schengen flight. Once checked in, proceed directly to security and passport control, have your travel documents ready and follow signage for your nationality or residence status. Keeping an eye on airport information screens and your airline’s app can also help you respond quickly if gate or timing changes occur.

Q6. Are British residents in Spain treated differently under the Entry/Exit System?
British citizens who are legal residents in Spain and hold valid residence cards are not meant to be recorded as short stay tourists in the Entry/Exit System. Recent guidance indicates that they should avoid EES kiosks and instead present themselves at staffed passport booths with both their passport and residence card. However, confusion and inconsistent implementation have meant that some residents have still found themselves directed into EES queues.

Q7. Does the Entry/Exit System affect travel within the Schengen Area?
No. The system applies at external Schengen borders when non EU nationals enter or leave the area. Flights and journeys that remain entirely within the Schengen Zone do not require EES checks, and passengers traveling on those routes generally experience no change at passport control compared with previous procedures.

Q8. Is this situation likely to improve soon?
Authorities say that current disruption is part of a transitional phase as staff are trained, software is updated and passengers become accustomed to the new procedures. If additional officers are deployed, kiosks become more reliable and signage is improved, waits should gradually shorten. However, with more peak travel periods ahead, there is concern that problems could reappear unless resourcing and planning keep pace with demand.

Q9. Are other Spanish airports facing similar Entry/Exit System problems?
Yes. While Malaga has attracted particular attention due to its heavy reliance on British and Irish tourism, travelers have reported queues and technical issues at other major Spanish hubs undergoing the Entry/Exit transition. The severity of disruption varies from airport to airport and day to day, often depending on passenger volumes, local staffing levels and how intensively the biometric kiosks are being used.

Q10. Should I consider changing my travel plans because of the Entry/Exit System issues?
Most passengers are still completing their journeys, albeit sometimes with longer waits at passport control, so there is no broad recommendation to avoid travel. Instead, experts advise adjusting your planning by arriving earlier, allowing more connection time where possible and staying informed about conditions at your departure airport. If you are particularly concerned about tight connections or traveling with vulnerable passengers, discussing options with your airline or travel agent may provide additional reassurance.