Migration is an energy-intensive phase of birds’ life cycle, often including the crossing of large ecological barriers on non-stop flights. The release of corticosterone (CORT), an adrenocortical hormone (also known as the stress hormone), generally rises at the onset of migration to facilitate and sustain high-energy metabolism. However, during prolonged flights, unfavourable meteorological events may affect the ability of migrants to cope with other stressors. In this study, we evaluated the effects of weather along the Mediterranean Sea on the physiological conditions of birds that reached a stopover island. We assessed fuel stores and CORT variations during pre-breeding migration in two trans-Saharan species, the Common Whitethroat (Curruca communis) and the Garden Warbler (Sylvia borin), upon arrival after the Mediterranean Sea crossing. By examining tailwinds and air temperature at different altitudes in the period preceding the arrival, we found that even with unfavourable weather conditions birds arrived at the stopover site with residual energy reserves. Also, adverse weather conditions did not influence baseline CORT levels. Interestingly, while both species exhibited a normal stress response to additional stressors, Garden Warblers showed peak CORT levels correlated with higher temperatures. These results suggest that migrants are generally well-equipped to handle variable weather conditions and may avoid migrating during extreme weather. As only birds surviving the sea crossing were studied, we suspect that most birds in poor condition did not reach the stopover site. Species-specific adaptations and diverse pre-migration ecological contexts may lead to different migration strategies to face this long-distance journey. Future research should explore to what extent physiological adjustments may aid migrants in dealing with the current increase in extreme meteorological events.