Europe’s New Digital Border Works for Security - But It’s Paralyzing Its Airports

That contradiction is becoming the real test of the system.

Security works. The border does not always

The case for EES is difficult to dismiss on security grounds. Since its launch in October 2025, the system has registered more than 160 million crossings across 29 participating countries and built a database containing more than 150 million records. More than 50,000 people have been refused entry, including more than 1,500 considered direct security threats to the Schengen area.

In February, the system helped identify a man attempting to enter Europe under three different identities.

For European law enforcement, this is a significant change. Instead of relying primarily on passport stamps and national border checks, member states now have access to a common digital record of travellers from outside the EU making short-term visits. Identity becomes something that can be checked against a European system rather than reconstructed at individual border posts.

Brunner has described EES as the world’s most advanced digital border system, arguing that it goes further than comparable arrangements in the United States and Canada. Under optimal conditions, processing a traveller’s profile takes about 30 seconds.

But a border system does not operate in optimal conditions.

That is where Europe’s problems have emerged.

At Frankfurt, Munich and Amsterdam’s Schiphol airport, waiting times have doubled to around two hours. At Zurich, Brussels, Alicante, Palma and Tenerife, queues have reached between three and five hours. Airports in Germany, France, Italy, Belgium, the Netherlands, Greece, Malta and Switzerland have temporarily deactivated automated biometric kiosks in an attempt to prevent the system from being overwhelmed by passenger flows.

The European Commission has therefore allowed countries to relax biometric collection during exceptional queues until September 6.

The deadline is now approaching.

Croatia shows what preparation can change

Croatia’s experience is important precisely because it complicates the argument that EES itself is unworkable.

The country activated the system one month earlier than required and equipped all 77 of its external border crossing points. Brunner called Croatia a leader in implementation. Croatian authorities have refused entry to more than 7,700 people considered security risks, while Božinović says irregular migration on the Croatian section of the route continues to decline.

There is an obvious lesson here, but it is not simply that other countries should copy Croatia.

Croatia’s external border is a controlled set of crossing points. Europe’s major airports are high-volume transport systems where border procedures compete with tight aircraft schedules, connecting passengers and the commercial expectations of airlines and travellers.

The difference matters.

A border checkpoint can be designed around the technology. An international airport has to absorb the technology without stopping the rest of the system.

EES has exposed a gap between those two requirements. The EU has created a common security architecture, but its physical infrastructure remains largely national and uneven. The result is a system that can work effectively at one border while producing bottlenecks at another.

That is less a technological failure than an institutional one.

The price of a digital Fortress Europe

The political pressure behind EES has also intensified.

The system is being introduced at a moment when European governments are under pressure to demonstrate control over external borders. The migration surge in Spain’s North African enclaves of Ceuta and Melilla earlier this month, involving an estimated 50,000 to 72,000 irregular crossings, has added urgency to that debate.

Brunner said the EU had “successfully passed the Ceuta test”. But the political reaction inside Schengen tells a more complicated story.

Italy and Finland called for the temporary suspension of Schengen rules in Spain, while Italy’s concerns have also made the removal of its internal checks on the border with Slovenia less likely. Slovenia has already removed its own controls on the Croatian border.

The paradox is becoming harder to ignore. Europe is strengthening its external border precisely as pressure inside the Schengen area encourages governments to reconsider internal controls.

Freedom of movement was built on the assumption that the external border could be managed effectively enough to make internal borders unnecessary. If the external system is overwhelmed - whether by migration pressure or by the infrastructure needed to process travellers - national governments have an incentive to bring controls back.

The digital border can therefore end up reinforcing the physical borders it was supposed to make less necessary.

Airports are becoming the weak link

The aviation industry has little patience for that trade-off.

Airlines and airport operators have criticised the design of EES, with Ryanair chief executive Michael O’Leary among the prominent critics. ACI Europe has also raised concerns about the operational consequences. Their preferred direction is to move more of the biometric registration process online rather than requiring the full procedure to take place at the airport.

Their concern is not merely about passenger inconvenience.

Airports operate on throughput. A delay at passport control can spread through terminals, affect boarding schedules and disrupt connections. When queues stretch to several hours, the consequences move beyond border management and into the economics of tourism and aviation.

That creates an unusual political coalition. Governments want stronger border controls. Security agencies gain from a common biometric database. But airports and airlines are effectively being asked to absorb the physical cost of a European security policy.

Travellers from outside the EU absorb part of it too.

The Commission’s flexibility mechanism is therefore more than a technical adjustment. It is an acknowledgement that the political ambition of EES currently exceeds the capacity of parts of the infrastructure expected to deliver it.

Eight EU countries and Switzerland are already seeking an extension beyond September 6.

Brussels now faces a difficult choice. Extend the flexibility and risk weakening the consistency of the new system just as it is being established, or insist on full implementation and risk turning airport congestion into a broader political problem.

Neither option is cost-free.

The border is moving beyond Europe’s airports

There is another part of the Croatian discussion that points to where EU border policy is heading.

Božinović argued that the scale of the Ceuta episode would have been impossible without Morocco’s involvement and called for stronger EU readmission agreements. He also pointed to Croatia’s experience and the involvement of Frontex in Serbia and Bosnia and Herzegovina.

That matters because European border policy is increasingly extending beyond the physical territory of the EU.

The logic is straightforward: if Europe can prevent irregular migration before it reaches an EU border, it puts less pressure on the border infrastructure itself. Frontex's cooperation with countries along the Balkan route becomes part of the same strategy as biometric registration at airports.

But it also changes the nature of European border management. Security increasingly depends on a chain stretching from third-country cooperation to external land borders, from databases to airports and from European agencies to national police forces.

The system only works as well as its weakest link.

Croatia can equip all 77 of its crossing points and demonstrate that EES can function effectively. That does not solve the problem at Schiphol or Frankfurt. Likewise, a highly capable airport system cannot compensate for a sudden migration surge at Europe’s external frontier.

The EU is therefore trying to build something larger than a new passport-control system. It is constructing a shared security infrastructure across a borderless internal market.

Its first year has shown that the security side of that project is becoming real. The unresolved question is whether Europe can build the physical and political capacity to carry it.

Because if the external border becomes more secure but the airports cannot process it, or if governments respond to external pressure by restoring internal checks, the problem will no longer be where Europe draws its borders.

It will be whether Schengen can still function between them.