The overall context of Indigenous peoples in the Brazilian Amazon has changed dramatically since the 1980s. After the adoption of the 1988 constitution, large tracts of Indigenous lands have been recognized, which now cover more than 21% of the Brazilian Amazon. Well conserved for the most part, they play a key role in deterring deforestation and in climate change mitigation, while also undergoing drastic economic and social changes. There are many factors challenging the sustainability of Indigenous territories today, including the deficient enforcement of Indigenous rights. The injunction that Indigenous peoples should protect the environment is complicating the definition of which economic activities they are entitled to develop inside their territories. The focus of this paper is to review the current situation of Indigenous territories in the Brazilian Amazon, providing historical context and pointing out current challenges and the debates surrounding their sustainability.