The goal of this article is to understand the contemporary transformations of indigenous territories in relation to several factors, including urbanisation, population growth, economic development and conservation policies. Using socio‐economic, governance and land use data, we explain the current territorial reorganisations of the Wayãpi and Teko indigenous peoples. We demonstrate the existence of an emerging ‘multi‐sited’ land use system that allows these indigenous peoples to benefit from resources in both urban and forest areas and ensures sovereignty over the territory. We emphasise the role of the delimitation of protected areas in catalysing identity claims and the process of land use reformulation.