Understanding factors that determine the distribution of the endangered Bonelli's Eagle requires different approaches and analytical tools. These factors may differ depending on the spatial scale at which they act. Bonelli's Eagle distribution in Spain has been studied previously using local and large (nation-wide) study area sizes, and human activities seemed not to affect negatively the occupancy of breeding territories. To study the factors affecting the species at an intermediate spatial scale we modelled Bonelli's Eagle distribution in Málaga province (S Spain), where the breeding density is the highest known in Europe. We applied a favourability function based on generalized linear models using the presence/absence of breeding territories of the species, and the values of a set of variables related to climate, topography, interspecific competition with Golden Eagle Aquila chrysaetos and human activity. We obtained a parsimonious model that included cliff availability and distance to highways as predictors of Bonelli's Eagle distribution. As highways may be seen as surrogates of intensive human activity, we conclude that, contrary to what was previously found at local or at nation-wide scales, human actions negatively affect the distribution of breeding territories at an intermediate scale. The construction of new roads and highways in the Mediterranean area of mainland Spain, which is the most climatically favourable region for the species, could have negative consequences for the Spanish metapopulation of Bonelli's Eagle, particularly in peripheral populations or distant areas that depend on the arrival of immigrants to persist.