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In this paper, the co-authors discuss how Indigenous theories are operationalized using an indigenist methodology grounded in intercultural collaboration. We describe the specific methodological considerations and methods that were incorporated into a decolonizing strategy for conducting research and co-creating knowledge with the Yine-Yami and Asheninka peoples of the Peruvian Amazon, including:(1) working with Indigenous co-researchers;(2) considering community members and federation officials as allies or collaborators instead of participants or researched subjects;(3) cultivating relational accountability and creating a research protocol by reflecting on the assumptions, motivations and values for conducting research with Indigenous peoples;(4) having each community ally identify desirable outcomes of the research;(5) sharing control of the design and delivery of the methodology; and (6) having collaborators validate co-created knowledge as the research was conducted. We argue that indigenist approaches are more appropriate frameworks for interacting with Indigenous peoples than methodologies typically deployed by Peruvian public organizations. With some adaptation, the methodology developed here could be used to conduct more respectful, meaningful and culturally sensitive research with Indigenous and historically oppressed groups