The EES glitch that could wrongly mark you as a Schengen overstayer – and how to fix it

The EU's new Entry/Exit System was supposed to make border checks smoother. Instead, some travellers are discovering a nasty side effect: their departure from the Schengen zone was never recorded, so the system thinks they never left.

The result? Days apparently keep accumulating after you've flown home, and the digital tally suggests you've blown the 90-days-in-180 rule. Consumer rights group Which? has flagged the issue, with dozens of readers reporting similar experiences. It even caught out British novelist Jojo Moyes, who visited Portugal in May and then learned on arrival in Marseille in October that her exit hadn't been logged. Officials told her she could face a €10,000 fine and a two-year Schengen ban unless the record was corrected.

For anyone who hasn't been following the rollout: the EES went live in October 2025 and became compulsory across 29 countries from 10 April this year. It replaces passport stamps with digital entries and exits, covering all EU states except Cyprus and Ireland, plus Iceland, Norway, Switzerland and Liechtenstein. The whole point was to automatically catch people overstaying the 90-day allowance for non-EU nationals.

The catch is that the system only works if every crossing is captured, and some exits are slipping through unrecorded. Worse, nobody will notify you that you've been flagged as an overstayer — many people only find out at a border desk, as Moyes did.

There is a way to protect yourself. You can check your recent days in the zone on the EES website, which shows your calculated stay over the past 180 days. If the number looks wrong, or the system reports 'incomplete data', you'll need to email the Data Controller for the country where the error happened — a list is published on the EES site. Attach a scan of your passport and evidence of your departure, such as a boarding pass or a bus or train ticket, so the record can be corrected.

Practical takeaway: if you're a non-EU traveller who limits yourself to 90 days in the zone, make a habit of checking your EES record shortly after each trip, and hold on to your outbound boarding passes until you've confirmed the exit was logged. It's a two-minute check that could spare you a five-figure fine and a two-year ban at the worst possible moment.