The Amarakaeri Communal Reserve is a sacred traditional territory of the Harakmbut culture located in the Peruvian Amazon. The management and planning processes in the reserve have been based traditionally on community and participatory processes. However, current trends and the processes of hydrocarbon exploitation are turning these traditional management systems into marginalized processes with low interest and involvement from the relevant governmental institutions. We evaluate the situation from a theoretical, practical and institutional point of view. We then propose a holistic perspective to approach this urgent subject in order to develop and implement management processes that avoid detrimental impacts on the community and the ecosystems in the area.