The native-original communities that live along the Andean mountain chain have managed, transformed and used the landscape for thousands of years. Signs of it are, e.g., the famous Inca road system and the different edaphic and hydraulic structures constructed in order to improve the local conditions for agricultural and pasturing activities; many of them are still in use. In this geographic space, impacts on the natural system directly affect the quality of life of these communities; many of them still maintain a traditional land use management, and others are in a transition process, towards a more industrialized use. During the last decades, this socio-ecosystem has been submitted to major pressure, caused by different internal and external drivers of environmental and social change. The Andes are the cradle of important civilizations, hotspot of biodiversity, home of native-original communities, important reserves of mineral/mining and energy resources, and of key ecosystems for climate change adaptation projects; that’s why they are placed in a situation of (potential) conflicts, between political, socioeconomic and environmental interests. In this context, the native-original Andean communities haven’t followed the pace of changes in their surroundings and their cultural and socioeconomic organization system have transformed precipitately. This can be evidenced in their current territory management, what has impacted their natural environment, accelerating the patterns of back coupling/feedbacks between the social and ecological systems. The conservation of biodiversity and ecosystem functioning in the Andes is linked to the adaptation and resilience of communal territory management systems. Understanding and learning about the implications of these kinds of territorial management of biodiversity allows us to identify points of inflection for the articulation of the conservation of biodiversity as integral part of communal territory management, and to complete the current strategies in conservation.