Abstract Background Migration phenology is shifting for many long-distance migrants due to global climate change, however the timing and duration of migration may influence the environmental conditions individuals encounter, with potential fitness consequences. Species with asynchronous migrations, i.e., with variability in migration timing, provide an excellent opportunity to investigate how of the conditions individuals experience during migration can vary and affect the migratory performance, route, and destination of migrants. Methods Here, we use GPS tracking and accelerometer data to examine if timing of autumn migration influences the migratory performance (duration, distance, route straightness, energy expenditure) and migration destinations of a long-distance, asynchronous, migrant, the white stork (Ciconia ciconia). We also compare the weather conditions (wind speed, wind direction, and boundary layer height) encountered on migration and examine the influence of wind direction on storks’ flight directions. Results From 2016 to 2020, we tracked 172 white storks and obtained 75 complete migrations from the breeding grounds in Europe to the sub-Saharan wintering areas. Autumn migration season spanned over a 3-month period (July–October) and arrival destinations covered a broad area of the Sahel, 2450 km apart, from Senegal to Niger. We found that timing of migration influenced both the performance and conditions individuals experienced: later storks spent fewer days on migration, adopted shorter and more direct routes in the Sahara Desert and consumed more energy when flying, as they were exposed to less supportive weather conditions. In the Desert, storks’ flight directions were significantly influenced by wind direction, with later individuals facing stronger easterly winds (i.e., winds blowing to the west), hence being more likely to end their migration in western areas of the Sahel region. Contrastingly, early storks encountered more supportive weather conditions, spent less energy on migration and were exposed to westerly winds, thus being more likely to end migration in eastern Sahel. Conclusions Our results show that the timing of migration influences the environmental conditions individuals face, the energetic costs of migration, and the wintering destinations, where birds may be exposed to different environmental conditions and distinct threats. These findings highlight that on-going changes in migration phenology, due to environmental change, may have critical fitness consequences for long-distance soaring migrants.