After decades of biomedical research on ayahuasca's molecular compounds and their physiological effects, recent clinical trials show evidence of therapeutic potential for depression. However, indigenous peoples have been using ayahuasca therapeutically for a very long time, and thus we question the epistemic authority attributed to scientific studies, proposing that epistemic injustices were committed with practical, cultural, social, and legal consequences. We question epistemic authority based on the double-blind design, the molecularization discourse, and contextual issues about safety. We propose a new approach to foster epistemically fair research, outlining how to enforce indigenous rights, considering the Brazilian, Peruvian, and Colombian cases. Indigenous peoples have the right to maintain, control, protect, and develop their biocultural heritage, traditional knowledge, and cultural expressions, including traditional medicine practices. New regulations about ayahuasca must respect the free, prior, and informed consent of indigenous peoples according to the International Labor Organization Indigenous and Tribal Peoples Convention no. 169. The declaration of the ayahuasca complex as a national cultural heritage may prevent patenting from third parties, fostering the development of traditional medicine. When involving isolated compounds derived from traditional knowledge, benefit-sharing agreements are mandatory according to the United Nations’ Convention on Biological Diversity. Considering the extremely high demand to treat millions of depressed patients, the medicalization of ayahuasca without adequate regulation respectful of indigenous rights can be detrimental to indigenous peoples and their management of local environments, potentially harming the sustainability of the plants and of the Amazon itself, which is approaching its dieback tipping point.