Climate change is rapidly challenging natural systems, ranking among the top drivers of biodiversity and ecosystem changes globally. Long-distance migratory bird species are particularly vulnerable to climate-induced changes and have already exhibited shifts in their distribution and phenology. In this study, we investigated the impact of climate change on the arrival fuel loads and stopover behavior of 16 trans-Saharan migratory passerines during spring migration aiming to highlight not only the direct effects on migration patterns but also the potential implications for later stages of their annual cycle. We showed that the double barrier crossing, i.e. the Sahara Desert and the Mediterranean Sea, imposes varying energy costs depending on geographic differences in the availability of stopover sites in northern Africa. The projected decline in the availability of these refueling sites is likely to pose a greater threat to migratory passerines than the changes in desert crossing distances. Moreover, arrival fuel load, migration timing, and, to a lesser extent, aridity, were found to influence stopover behavior. However, with deteriorating conditions across the Mediterranean, aridity is expected to play a more significant role in stopover behavior in the future. The predicted delays in the timing of migration and the reduction of arrival fuel loads could ultimately compromise the breeding success of these birds or even increase mortality en route. The study emphasizes the vulnerability of migratory birds to climate change and provides valuable insights for conservation planning, highlighting the need to protect critical refueling areas. [ABSTRACT FROM AUTHOR]