Europe's New Border System Causes Double the Missed Connections

European airports are experiencing a significant increase in missed flight connections due to delays at border control, with the number of passengers unable to make their connecting flights doubling over the summer. This surge is attributed to the new Entry/Exit System (EES), a biometric border control system implemented across the Schengen Zone. The EES, which began its phased rollout in October 2025 and became fully operational at external borders on April 10, 2026, replaces passport stamps with digital records of entry and exit, including facial photos and fingerprints, for non-EU citizens. While intended to streamline border checks, the system has led to longer processing times, with passport checks now taking approximately 90 seconds compared to the previous 20-25 seconds, according to the International Air Transport Association (IATA).

Major European airports have seen peak waiting times double in some cases. For instance, Frankfurt Airport's peak wait time in July reached 120 minutes, up from 60 minutes the previous year, while Munich and Amsterdam also experienced significant increases. These extended delays, particularly during peak hours, are causing passengers to miss their connecting flights. Initially, Schengen countries could temporarily suspend biometric data collection during excessive queues, a measure described as a "safety valve" by the aviation industry that helped mitigate issues over the summer.

However, this flexibility ended on September 6. Nine countries, including Germany, France, and Italy, had requested an extension from the European Commission to continue this temporary suspension, citing "serious difficulties" with the EES under high load. Aviation bodies like IATA and ACI Europe had also urged for a delay in the full implementation until late October 2026. As of September 6, the European Commission had not officially extended the mechanism, though implementation remains uneven in some airports due to ongoing technical problems.

Israeli travelers are particularly advised to be cautious. Those connecting through a Schengen airport where they must undergo border control, such as flying from Tel Aviv to Frankfurt and then onward to another Schengen destination, face increased risk. Experts recommend avoiding itineraries with minimal connection times if Schengen border control is required during the layover. Passengers cannot mitigate this risk by arriving earlier at their departure airport, as the delays occur upon arrival in Europe. It is important to distinguish the EES from the upcoming ETIAS (European Travel Information and Authorization System), a separate travel authorization system for visa-exempt countries, including Israel, scheduled for late 2026.