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Unmasking the ecological processes responsible for the dynamics of a population is a necessary step toward understanding its threats and viability. We examined a fitness proxy (reproductive success) of an endangered raptor in relation to its ecological niche and spatial distribution to provide insights into the dynamics and potential threats to the population. We first studied how biotic and abiotic conditions drive both the spatial distribution of Bonelli's eagle (Aquila fasciata) and its long-term reproductive success in a large area of northwestern Spain. We focused on the relationship between these two characteristics of the population. Our results showed that biotic factors (occurrence of competitors such as the golden eagle or prey availability) were more associated with the spatial distribution of the species than with its reproductive success. In contrast, abiotic factors describing climate were linked to reproductive success. Most interestingly, we found a mismatch between spatial suitability and reproductive success because reproduction was compromised in the areas that were more suitable for the occurrence of the species. The results suggest that productivity (less than one chick per year), measured as long-term reproductive success, may compromise the population viability and suggest the presence of an underlying mechanism in the population. Our results highlight the benefits of simultaneously considering both large-scale spatial distribution patterns and measures of fitness, which often require larger investments of time, for endangered species conservation programs.