ABSTRACT This paper discusses the transformations in the relationship between the Goeldi Museum and Indigenous peoples, specifically the Mebêngôkre, better known as Kayapo, in a long-term perspective. Their complexity is not merely influence of a social Darwinism that would have cornered natural history museums in the role of agents of colonialism and ideologues of structural racism. Three key moments in the construction of ties between the Goeldi Museum and the Mebêngôkre are analyzed: the transition from the 19th to the 20th century, when religious missions were financed by the State and compulsory intermediaries between the Indigenous people and national society to integrate them into ‘civilization’; the 1930s, when new migratory movements to the Amazon region and the dictates of an oligarchy that strengthened itself through land control - especially in Brazil nut production areas - threatened the physical and territorial integrity of this people; and, finally, the 1980s-1990s, when opposition to the developmentalism of the military regime emerged and crystallized into a socio-environmental model that recognizes the importance of the role of Indigenous peoples and traditional populations in the Amazon. After highlighting the transformations observed in the relationship between museums and Indigenous peoples, the article concludes by advocating the importance assumed, in the 21st century, by collaborative research and participatory museology, both for their scientific qualification and for the appreciation of Indigenous knowledge with profound political, social, and environmental repercussions.