Abstract The recent development of tracking technologies has allowed to discover how small migratory birds cope with large ecological barriers such as seas and deserts, displaying remarkable behaviors like extreme diel flight altitude changes when crossing the Sahara Desert. However, the drivers and the prevalence of such behaviors among terrestrial migrants remain understudied. By deploying multi-sensor loggers on 59 individuals from 16 species in southern Europe, and using methods of geo-positioning integrating light, pressure, and activity data, we investigated where, when, and how small, nocturnal, migratory birds crossed two types of ecological barriers: two marine areas (the Bay of Biscay and the Mediterranean Sea) and one desert (the Sahara Desert). We found that sea crossings were often performed at very low altitude, close to sea level. Conversely, flights over the Sahara Desert typically reached median altitudes of 3000-4000 meters above sea level. These flights often lasted throughout the entire night (50% of the time) or extended up to 45 hours. Species with longer wings tended to cross the Sahara at higher altitudes. We also highlighted changes of flight altitudes between night and day in prolonged flights over the Sahara Desert in 13 species and showed that these changes do not correspond to the search for constant temperature conditions nor supporting winds. Nevertheless, during these flights, we found that birds tend to take advantage of supporting winds by flying at higher altitudes and make more significant changes of altitude when the air temperature is warmer. These changes in altitude, which coincide with sunrise, support the hypothesis that birds reach high altitudes during daytime to mitigate the effect of extra heating from solar radiation. Our study describes the flight strategies of several species crossing different types of ecological barriers and offers new insights into the dynamics of flight altitudes of small migratory birds crossing the Sahara Desert. It also confirms that the heat balance of a flying bird is complex, with several factors interacting, and calls for further research, including experimental studies, to unravel the role of each of these factors.