Capsule There is a relationship between owl numbers and the availability of the agri-forest patchwork. Aims To model habitat preferences at three different scales of two predators largely neglected within the framework of Environmental Impact Assessment (EIA) studies. Methods We studied habitat preferences of Long-eared Owls and Little Owls by comparing habitat composition around 28 and 78 occupied territories respectively with 55 non-occupied territories in Alicante (eastern Spain). Generalized linear models were used to examine patterns of habitat preference at three different spatial scales: nest-site, home range and landscape. Results At the nest-site scale, Long-eared Owls preferred wooded areas with few paved roads while Little Owls preferred arid plantations. Furthermore, the probability of finding an occupied territory increased with the proximity of another occupied territory in the surroundings. The home range scale models mirror the feeding requirements of the owls. Thus, Long-eared Owls occupied areas with high percentages of forest, arid plantations, edges between these two land uses, short distances between nests, with presence of conspecifics and little human disturbance. Little Owls occupied arid plantations with high availability of linear structures and the proximity of villages. At the landscape scale, Long-eared Owls eluded extensive forests, and Little Owls preferred arid plantations. Conclusions We suggest a hierarchical process of habitat selection for both owls regarding fitting trophic resources at the broadest scales and adequate sites for breeding and roosting at the smallest scale. EIA studies must consider that protecting small areas around single nests may not be an efficient conservation option compared with preserving clusters of territories for both species.