Bonelli’s Eagle Hieraaetus fasciatus and Golden Eagle Aquila chrysaetos are two declining species, in which floaters tend to be located outside of breeding territories during the dispersal period, in so-called settlement areas. We studied settlement areas for both these long-lived raptors in the southern Iberian Peninsula, to gain a better understanding of the ecological requirements of the eagles during their long pre-adult stage, a period accounting for around 80% of the species’ mortality. Eagle abundance was calculated by road censuses, and habitat characteristics of settlement and non-settlement areas compared by General Discriminant Analysis (GDA) and Logistic Regression (LR). The best model of GDA and LR incorporated the abundance of main prey for eagles (rabbits, partridges) and orchard surface area, and explained 100% of eagle presence; the best model selected by GDA also included habitat heterogeneity. Both eagles tended to share settlement areas in the southern Iberian Peninsula and, when they did not, the mean annual temperature and slope appeared to explain the segregation between the two species. Management measures for the conservation of both threatened species during the dispersal period should be focused on identifying settlement areas, maintaining high prey densities and maximum habitat heterogeneity.