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During spring migration, nocturnal migrants attempt to minimize their travel time to reach their breeding grounds early. However, how they behave and respond to unfavourable conditions during their springtime travels is much less understood. In this study, we reveal the effects of atmospheric factors on nocturnal bird migration under adverse conditions during spring and autumn, based on one of the most detailed bird migration studies globally, using radar data from 13 deployments over a period of seven years (2014–2020) in the Levant region. Using ERA5 reanalysis data, we found that migratory birds maintain similar ground speeds in both autumn and spring migrations, but during spring, when encountering unfavourable winds, they put more effort into maintaining their travel speed by increasing self-powered airspeed by 18%. Moreover, we report for the first time that spring migrants showed less selectivity to wind conditions and migrated even under unfavourable headwind and crosswind conditions. Interestingly, we discovered that temperature was the most important weather parameter, such that warm weather substantially increased migration intensities in both seasons. Our results enhance our understanding of bird migration over the Levant region, one of the world’s largest and most important migration flyways, and the factors controlling it. This information is essential for predicting bird migration, which—especially under the ongoing anthropogenic changes—is of high importance.