Understanding ecological requirements of animals is essential to improve habitat management and conservation strategies for endangered species. However, as most studies on Golden Eagle's habitat preferences and breeding ecology have been conducted in northern latitudes (e.g. USA, Scotland, Scandinavia and the European Alpine region), our knowledge of the species ecology in the Mediterranean basin is more limited. Currently, only 16 pairs still remain in Sicily (southern Italy) and in spite of this delicate status of conservation, there were no previous attempts to analyse ecological requirements of the species in the island. Therefore, we monitored Golden Eagles from 1990 to 2012, analyzed habitat characteristics of breeding territories and quantified habitat relationships with breeding performance. We used a case-control design through Generalized Linear Models to examine ecological descriptors at two different spatial scales: (i) “territory” defined as a plot of 4 km radius centered in the nesting area; and (ii) “landscape” by means of the 10 × 10 km Universal Transversal Mercator (UTM) cells where the species was present or absent. At the territory scale, the presence of Golden Eagle was positively related to the ruggedness of the terrain and to the extension of arable land, and negatively to the extension of forests. At the landscape scale the presence of the species was positively correlated with the range of slope and negatively to the aridity of the surrounding landscape and the extension of forest areas. The Golden Eagle has experienced a strong decline in breeding performance during the last two decades in Sicily, which negatively impacted population dynamics. The best model at the territory scale included the surface of sparsely vegetated areas (i.e. a surrogate of prey availability) as the best predictor of breeding output (i.e. number of young fledged). At the landscape scale, the best predictor of breeding output was the average annual temperature (positive effect) and surface of artificial lands (negative effect). Significant differences in environmental characteristics were found between occupied and unoccupied sampling units and between territories of high and low breeding performance. Our results highlight the importance of maintaining the structure of landscape arising from traditional forms of extensive agriculture in the Mediterranean basin, thereby favouring prey availability, and the importance of limiting human activities and changes in land use in rugged mountainous areas.