Identifying threats to declining species and prescribing ways of preventing their extinction are basic challenges for biodiversity conservation. We analysed the causes underlying the loss of territories of the Endangered Egyptian vulture Neophron percnopterus in a key population at the north-western edge of its distribution in Europe by developing multi-scale models that combined factors from nest site to landscape. We used generalized linear models and an information-theoretic approach to identify the optimal combination of scales and resolutions that could explain territorial abandonment. Those models combining nest-site and landscape scales considerably improved prediction ability compared to those considering only one scale. The best combined model had a high predictive ability (96.9% of correctly classified cases). Small cliffs at high altitudes in rugged areas with declining livestock (especially of sheep and goats) increased the likelihood of territory abandonment. Our findings highlight the importance of developing region-specific multi-scale models to determine reliably the factors driving territory loss and of designing effective conservation strategies accordingly. Conservation measures for the studied population should be developed at two spatial scales. At the smaller scale it is necessary to closely control nest sites to avoid direct disturbances. At a larger scale it is essential to implement policies that can support traditional pastoralism.