Here we explore the environmental and geographical factors affecting the winter distribution of the black stork Ciconia nigra in the Iberian Peninsula, where an increasing number of individuals have remained to winter in the last two decades. We recorded 179 locations of 54 ringed individuals between 1988 and 2011 to map the species habitat suitability with MaxEnt, a machine-learning technique based on the principle of maximum entropy. The migratory movements of 25 birds equipped with satellite transmitters were used to define the autumnal migratory flyway used by most storks crossing the Peninsula as well as to define the wintering period. The aim was to test if the number of wintering storks was positively correlated to habitat suitability and negatively correlated to the flyway distance. Data provided by an extensive count across Portugal and Spain during the 2012–2013 winter supported the findings that black storks were more abundant in areas of high habitat suitability close to the migratory flyway. This agrees with previous evidence on the role of migratory flyways in determining the distribution of some wintering birds in Iberia. A gap analysis reflected that just 12.3% of the suitable areas and 18.8% of individuals recorded during the 2012–2013 winter were included within the Special Protection Areas network of Portugal and Spain. Most of these birds were crowded in unprotected areas covered by rice fields (68% of individuals), a key habitat for the species.