In the southernmost Andean regions of Peru, Moquegua, and Tacna, close to Chile and Bolivia borders, large forest stands of Polylepis species are essential for the social, economic, and environmental functionality of six basins. However, the need for more knowledge about their ecology, limited conservation efforts, and insufficient technical capacities for territorial regulation could accelerate their structural and functioning deterioration. Using landscape ecology -interdisciplinary science shaped by geography and biology- we found that in four evaluated areas, the composition of birds (and therefore also the resources they use) is differentiated by the influence of landscape fragmentation. Only two protected areas were legally recognized in the region, but they were established to cover small and remote isolated territories, which makes it challenging to conserve them effectively. Due to the poverty conditions common among the local communities, extractive or pastoralist activities conducted in large areas can trigger higher forest fragmentation rates. Under these circumstances, the valuable ecosystem services in the study area would be permanently lost or maintained at high risk. Because of these risks, specific measures were proposed to improve the social-environmental management of the forest by implementing mechanisms aimed at generating sustainable economic benefits in a healthy environment and social peace.