Since 2005, the Putumayo organization collaborates with the local indigenous organizations of the Kichwa (FIKAPIR) and the Secoya (OISPE) to strengthen their federations. These federations contribute to the protection of the territorial integrity and the cultural identity of their people. Putumayo supports the organizations logistically and administratively as well as on more fundamental matters, in order to enhance internal cohesion and external strength.

Every year, Putumayo supports the congress of FIKAPIR and of OISPE where important subjects are discussed like cultural identity, natural resources and conservation, indigenous territories and rights, leadership, urgent needs of the communities and threats to a sustainable livelihood. The Board of Directors of the federations evaluates its activities and the action plans for the following year are formulated and discussed.

Legal expertise and logistic support are provided to FIKAPIR and OISPE to achieve a legal status. This is a necessary condition to be recognized by the Peruvian authorities as an official organization. In a first phase the statutes were drafted by the communities themselves. Subsequently the statutes were checked on their legal conformity and improved where necessary by an expert on indigenous rights in Lima. After a last review by the communities the statutes of FIKAPIR will be registered.

Putumayo also offers general capacity building and information sessions, mostly during the congresses of the federations. Different topics are dealt with such as indigenous rights, extraction of natural resources, indigenous territory, leadership and organization. Through weekly telephone reunions with the leaders of the federations, information is shared on decisions and the latest news communicated to the indigenous communities.