Indigenous communities living in Arauca department, a region located on the Eastern Plains of Colombia, are at an imminent risk of physical and cultural extermination -according to the orders 004 and 382 from the Constitutional Court of Colombia- due to a double vulnerability which stems from a historic structural violence dating from the creation of the nation-state and direct violence as a consequence of armed conflict. The physical extermination refers to the high mortality rates that this population suffers either by violence or natural death, while the cultural extermination is a result of both an accelerated process of acculturation and a progressive loss of culture, territory and respect from traditional authorities. This study, by analyzing the local context and the actions that have done harm, addresses the best practices for humanitarian interventions over the role of territory, culture, governance and autonomy as key factors for empowering community members to overcome, face or diminish the consequences of these vulnerabilities.