Background: Current literature emphasizes the need to implement informed consent according to indigenous principles and worldviews. However, few studies explicitly address how informed consent can be effectively and appropriately obtained in indigenous communities in accordance with research ethics guidelines. Methods: This article uses participatory rural appraisal methods to identify and characterize community preferences for informed consent in two indigenous communities in the Peruvian Amazon, using Canadian federal research regulations and McGill University's Research Ethics Board as a case study to examine where institutional ethics guidelines constrain or support culturally appropriate notions of informed consent. Results: The study emphasizes the importance of tailoring informed consent procedures to community circumstances. Although both communities in this case study are located in the Peruvian Amazon, there were important distinctions between them, such as gender dynamics and social structure, which profoundly affected informed consent procedures. It is also important to consider the balance of collectivism and individualism at a community level in order to determine the role of individual and community consent. Conclusion: Research ethics guidelines generally allow for this contextualized approach. However, regulations still have the potential to constrain indigenous informed consent due to content requirements for informed consent forms, limited flexibility for modifications in the field, and requirements for individual consent.