Apex predators make excellent bioindicators of habitat quality and anthropogenic changes. Eagle owls (Bubo bubo) are such apex and keystone predators, who show preferential nest-site selection, usually away from human activities and habitation. However, Israel is a small country with a burgeoning human population. Hence, in order to understand the habitat requirements of eagle owls in central Israel, we conducted a multi-scale model analysis on their existing nest sites between 2006 and 2010. We identified 203 successful breeding attempts at 73 different sites. Our data suggested that the breeding population of the eagle owls was limited by the availability of quality nest locations, i.e., quarries, and caves. The probability of an eagle pair breeding increased with the presence of both quarries and caves, but was not related to mesohabitat properties. In addition, eagle owl breeding densities were positively related to the number of nest localities and to the planted woodlands. Furthermore, we found that eagle owls successfully raised their young regardless of the surrounding mesohabitat and sought the presence of other potential nest sites in the vicinity of the active nest sites, most likely due to the owls’ opportunistic and generalist hunting behavior, which facilitated the consumption of a wide prey base. Appropriate nest sites (quarries and caves) appeared to increase population numbers and, therefore, should be protected Further studies should determine whether increasing artificial nest sites and reclaiming abandoned quarries could increase eagle owl numbers in a sustainable manner.