Habitat preference of eagle owls Bubo bubo were examined through comparing habitat composition around 51 occupied cliffs and 36 non-occupied cliffs in Alicante (E Spain). We employed Generalized Linear Models to examine patterns of habitat preference at three different spatial scales: nest site (7 km2), home range (25 km2), and landscape (100 km2). At the nest site scale, occupied cliffs were more rugged, had a greater proportion of forest surface in the surroundings, and were further from the nearest paved road than unoccupied cliffs. Additionally, probability of having an occupied cliff increased when there was another occupied territory in the surroundings. At both the home range scale and the landscape scale, high probabilities of presence of eagle owls were related to high percentages of Mediterranean scrubland around the cliffs, which are the preferred habitat of European rabbits Oryctolagus cuniculus, the main prey of the owls. We suggest a hierarchical process of habitat selection in the eagle owl concerning suitable trophic resources at the broadest scales and adequate sites for breeding and roosting at the smallest scale. However, it should be noted that some structural features such as the proximity of roads were not necessarily avoided by the owls, but their presence were possibly constrained by systematic killing of individuals. Our paper provides new evidence for the requirement of multi-scale approaches to gain insight into both the different limiting factors for the persistence of populations and the role of individual perception of the environment in the evolution of habitat selection.