Aerial migrants commonly face atmospheric dynamics that may affect their movement and behaviour. Specifically, bird flight mode has been suggested to depend on convective updraught availability and tailwind assistance. However, this has not been tested thus far since both bird tracks and meteorological conditions are difficult to measure in detail throughout extended migratory flyways. Here, we applied, to our knowledge, the first comprehensive numerical atmospheric simulations by mean of the Regional Atmospheric Modeling System (RAMS) to study how meteorological processes affect the flight behaviour of migrating birds. We followed European bee-eaters (Merops apiaster) over southern Israel using radio telemetry and contrasted bird flight mode (flapping, soaring-gliding or mixed flight) against explanatory meteorological variables estimated by RAMS simulations at a spatial grid resolution of 250 × 250 m(2). We found that temperature and especially turbulence kinetic energy (TKE) determine bee-eater flight mode, whereas, unexpectedly, no effect of tailwind assistance was found. TKE during soaring-gliding was significantly higher and distinct from TKE during flapping. We propose that applying detailed atmospheric simulations over extended migratory flyways can elucidate the highly dynamic behaviour of air-borne organisms, help predict the abundance and distribution of migrating birds, and aid in mitigating hazardous implications of bird migration.