The destruction of tropical forests is an environmental issue of global significance. This process has deep historical roots, with recent scholarship exploring the role of European colonisation and capitalist expansion in driving tropical deforestation from the sixteenth century onwards. Less attention, however, has been given to how Indigenous resistance has impeded deforestation over this time period. Here we analyse how non-state Indigenous groups obstructed Spanish and Portuguese political control and commodity frontiers in tropical South America. Drawing on archival sources, together with Indigenous Guaraní and Paiter Suruí philosophy and oral history, we assess this phenomenon in two biomes, the Atlantic and Amazon Rainforests. The results highlight that over the longue durée, Indigenous resistance has assisted in the conservation of South American tropical forests, acting as a significant—but under-recognised—factor in both regional and global environmental history. This history is of particular importance given the increased recognition of the role of Indigenous peoples in conserving tropical forests as carbon sinks in the twenty-first century.