Internal factors such as experience (e.g. age) and motivation for breeding, and external ones such as environmental conditions (e.g. meteorology and landscape characteristics) can promote differences in migratory behaviour and routes among seasons, regions and populations. Using satellite telemetry we investigated whether such differences occur and which factors promote them among migrating Eleonora’s falcons breeding in the Mediterranean area (Spain and Croatia) and wintering in Madagascar. We found that during autumn migration no age differences occur when crossing the Sahara desert, but in the remaining African regions, juveniles were more prone than adults to fly at a slower and more tortuous rate, as well as exhibiting longer stop-overs, particularly in the Sahel region. Such differences might be promoted by a lower foraging and pre-migratory fattening efficiency in juveniles. During spring, routes were significantly more eastern than during autumn, resulting in a loop migration occurring in all studied populations. This could be accounted by seasonal variation in the distribution of trophic resources. Our results show that Eleonora’s falcons integrate spatially seasonal changing resources on a continental scale throughout their annual cycle, changing their movement patterns in response to internal (age) and external (habitat) factors. This loop migration pattern may prove to be widespread among other Palearctic trans-continental migratory bird species.