Species life history and anthropogenic influence are important drivers of population performance and viability in human‐dominated ecosystems. How these factors affect habitat selection and occupancy in long‐lived species is an important topic for their conservation. Long‐term datasets are needed for establishing the underlying drivers of this process. In this 22 year‐long study, we conducted annual surveys of Bonelli's eagle in the east of the Iberian Peninsula. During this period, 42.8% of the known territories remained unoccupied. Territories with a higher likelihood of raising two chicks over time were stable, evidenced by a lower coefficient of variation in productivity, and were more likely to remain occupied. Moreover, territories with lower habitat diversity, dominated by coniferous forest or agricultural fields, and those located further away from the coast and at higher altitudes showed lower rates of occupancy (i.e., unoccupied >3 consecutive years). To validate these associations, we monitored space use of 22 individuals equipped with Global Positioning System/Global System for Mobile (GPS/GSM) transmitters, which confirmed that eagles selected for open habitats (mainly scrublands and transitional woodland‐scrubs) intermixed with forest areas within their home ranges. In contrast, individuals avoided areas dominated by agricultural, urban, and continuous forests for breeding in line with the observations for unoccupied territories. Our results highlight the important interplay between natural and anthropogenic factors, which also have important implications for other raptor species. Preservation of the most productive territories and the re‐occupancy of unoccupied territories along with reducing threats in the preferred habitats are fundamental actions that should be taken immediately to sustain viable populations. Potential management actions include enhancing natural prey density through habitat restoration and conservation, mitigating threats and reducing mortality risks due to power lines, fences, poisoning, and maintaining habitat heterogeneity important to eagles' hunting activities.