EES queues hit five hours at Brussels Airport

Non-EU travellers arriving at Brussels Airport waited up to five hours at passport control during the week of 21–27 September 2026, and around 600 passengers missed their flights over four days. The airport confirmed the figures on 29 September and is now pressing the Belgian Federal Police for full staffing at all border desks, renewed e-gate access for eligible third-country nationals, and more flexibility in how the Entry/Exit System is applied during congestion.

What caused the five-hour waits?

Two things hit at once. First, EES continued to create a longer first-time registration process for every non-EU short-stay visitor who had not previously enrolled: fingerprints, a facial scan and travel-document capture at a staffed desk, which takes five to ten minutes when everything works and considerably longer when the system runs slowly. Second, a change to how pre-registration kiosks operate removed a step that had let eligible travellers from countries such as the United States partially complete their check before joining the desk queue. More people needed a full staffed-desk appointment, and there were not enough open positions to absorb the load.

The Entry/Exit System has been fully operational across all Schengen external borders since 10 April 2026. Brussels Airport is not an outlier. Frankfurt, Amsterdam Schiphol and Paris Charles de Gaulle all reported peak waits of several hours during the summer. What makes the Brussels week significant is that it came after the worst summer congestion had eased, and after the emergency biometric-pause mechanism that nine countries used to manage peak queues formally expired on 7 September. September is supposed to be easier. Waits of five hours in the fourth week of September suggest the system has not yet stabilised.

What is Brussels Airport asking for?

In its statement, the airport named three specific requests. Full staffing of all Belgian Federal Police border-control positions is the most urgent: some desks have been running short-handed, which compounds the bottleneck created by EES enrolment times. The airport is also calling for eligible third-country nationals to regain access to e-gates where their passport permits it, a measure that was available before full EES implementation but has been restricted at some Schengen entry points. Finally, it wants the European Commission to give airports more operational flexibility to manage surges, particularly when a technical problem with the EES system slows individual registrations.

Belgian Federal Police said additional officers are being trained and that it is working to increase coverage at the passport desks. No specific completion date for that training was given.

How does this compare to other airports this autumn?

The picture across Schengen in autumn is genuinely better than it was in July and August. The proportion of travellers who have already completed EES biometric enrolment grows with every wave of arrivals, and repeat crossings are faster. The broader autumn queue outlook explains how enrolment numbers are changing the dynamic at busier airports. Brussels is a particular pressure point because it is a major connecting hub for long-haul passengers from North America and sub-Saharan Africa, many of whom are arriving in the Schengen Area for the first time. Those passengers require the full registration process regardless of how busy the desks are.

What does “not enrolled” mean for your trip?

If you have not crossed a Schengen external border since 12 October 2025, you are not yet enrolled. At Brussels Airport that means joining the staffed-desk queue, not the e-gate line, and building in extra time accordingly. Arriving during off-peak hours helps: the worst queues at most Schengen airports concentrate on morning arrivals from overnight transatlantic and Gulf flights. Once enrolled, subsequent crossings are substantially faster, though the exact benefit depends on which crossing and whether e-gates are available for your passport nationality.

If you have a connecting flight at Brussels, the standard advice of a minimum two-hour connection for a Schengen entry now looks optimistic during busy mornings. Experienced travel agents have been recommending three hours or more for first-time enrollees transiting through the airport.

Does this affect ETIAS?

Not directly. ETIAS is not yet in operation and no applications are open anywhere. The current entry requirement for visa-exempt travellers is a valid passport and nothing more. But the Brussels queues are a reminder of why the EU has been cautious about adding a second border system before EES is running smoothly. The next governance milestone for ETIAS is the eu-LISA management board meeting in Dublin, 17–19 November 2026. For the current official position on timing, see the ETIAS status page.