Conservation of migratory species faces the challenge of understanding the ecological requirements of individuals living in two geographically separated regions. In some cases, the entire population of widely distributed species congregates at relatively small wintering areas and hence, these areas become a priority for the species' conservation. Satellite telemetry allows fine tracking of animal movements and distribution in those less known, often remote areas. Through integrating satellite and GPS data from five separated populations comprising most of the breeding range, we created a wide habitat suitability model for the Eleonora's falcon on its wintering grounds in Madagascar. On this basis, we further investigated, for the first time, the impact of climate change on the future suitability of the species' wintering areas. Eleonora's falcons are mainly distributed in the north and along the east of Madagascar, exhibiting strong site fidelity over years. The current species' distribution pattern is associated with climatic factors, which are likely related to food availability. The extent of suitable areas for Eleonora's falcon is expected to increase in the future. The integration of habitat use information and climatic projections may provide insights on the consequences of global environmental changes for the long-term persistence of migratory species populations.