Schengen’s EES system flags over 4,000 overstays in the first 4 months: how it works and what it could lead to

In its first four months of operation, the EU’s new digital border control system — Entry/Exit System (EES) — recorded more than 4,000 cases of stays beyond the allowed limit in the Schengen area. The figures were released by the European Commission.

The EES went live on 12 October 2025, replacing the familiar manual passport stamps. Now, for third-country nationals (not EU citizens) entering Schengen for short stays without a visa, the system applies biometric registration of entries and exits.

At a February 23 briefing in the European Parliament (LIBE committee), Commission representative Henrik Nielsen said that, over the period, the system processed around 17 million travellers and recorded roughly 30 million border crossings.

During the same timeframe, about 16,000 people were refused entry. Around a quarter of these refusals were linked to individuals whom the system flagged for breaching the 90/180-day rule — staying up to 90 days within any 180-day period.

How EES works and what it actually checks

EES collects biometric data, including fingerprints and facial scans, to log the entry and exit moments of third-country nationals. Based on this information, the system automatically calculates how long a person actually stayed in the Schengen area, ensuring compliance with the 90 days in any 180-day period limit.

Previously, enforcement of the 90/180 rule depended largely on border officers manually checking passport entry stamps. The European Commission stressed that this approach does not always reliably identify people who overstay.

EU IT agency EU-LISA Executive Director Tillmann Keber said that the rollout across the EU is proceeding steadily and the system is fully operational.

Phased rollout and uneven results on the ground

EES is being implemented in stages. Initially, border authorities registered roughly 10% of eligible travellers. Coverage then increased: to at least 35% from 9 January 2026, and to 50% from 10 March. Full coverage is planned for 10 April, after which passport stamps for short stays will be discontinued.

In practice, however, the airport rollout has been more challenging. At Paris Charles de Gaulle, delays were reported due to kiosk malfunctions, software issues, and staff shortages. In Lisbon, operators temporarily reverted to manual stamping after biometric checks triggered serious queues.

Airport operators warn that processing times at the border could rise by up to 70% in locations where the system is already running. Peak waits of up to three hours have also been reported.

Why EES matters beyond catching overstayers

EES data also feeds into broader control mechanisms. This includes the revised visa-suspension mechanism that took effect in December 2025. The threshold for suspending visa-free access for Schengen countries was lowered: from 50% growth in the share of violations to 30%.

Before EES, measuring the level of overstays with sufficient accuracy was difficult: in digital form, such country-level data was essentially not available.

Now, as the system processes millions of trips and automatically flags violators, the situation changes. Brussels receives biometrically verified information in a more “transparent” way: which nationalities are overstaying, how often it happens, and by how many days.

In addition, the updated mechanism added citizenship by investment (CBI) as a separate possible ground for suspending visa-free travel. In its latest report, the European Commission noted that the operation of CBI programmes “in itself” may be considered a reason for suspension.

The most direct impact, according to estimates, may affect five Eastern Caribbean countries with active CBI programmes: Antigua and Barbuda, Dominica, Grenada, Saint Kitts and Nevis, and Saint Lucia.

In March 2026, under the updated rules, Georgia was the first country to come under scrutiny. The European Commission suspended visa-free travel for holders of Georgia’s diplomatic, service, and official passports. The grounds were linked to democracy and human-rights concerns rather than overstays, but the decision itself showed that the new powers are already being used.

CBI countries and a “layered” approach to control

For CBI jurisdictions, EES is only one element in a broader, more complex monitoring framework. The next step will be ETIAS (European Travel Information and Authorization System) — a pre-travel screening tool for visa-exempt travellers — planned for the end of 2026 and mandatory by October 2027.

If EES identifies who is already in Schengen, then ETIAS will determine who can enter. According to an IMI survey of investment migration leaders, one third of respondents believe ETIAS could become an instrument for discriminating against holders of passports obtained through CBI.

The concern is that EU authorities may use algorithmic screening to enforce practical restrictions “in practice,” while formally keeping visa-free status.

In 2024, Caribbean countries with CBI programmes carried out regional reforms: they introduced mandatory interviews, strengthened due diligence, and created a unified regulatory body. However, whether these steps are enough for Brussels remains unclear: the Commission’s rhetoric, in effect, has shifted from calls for reforms to discussions about their possible termination.

What risks face people who overstay

Travellers who remain in Schengen beyond the permitted period may face different types of liability: from fines (for example, €198 in France) to recorded violations that could affect future visa applications. In the most serious cases, authorities may issue a deportation order or impose a temporary entry ban, although such measures are reportedly rare at the early stage of EES implementation.

There are exceptions for situations not caused by the individual, such as serious illness.

At the same time, third-country nationals holding long-stay visas or residence permits are not registered in EES. Still, during the system “ramp-up” period, additional queues at Schengen borders are possible.

Our Telegram channel about various types of Greek residence permits, digital nomad programs, and the Greek Golden Visa: @digitalnomadgr