During the last two decades, new archaeological projects which systematically integrate a variety of plant recovery techniques, along with palaeoecology, palaeoclimate, soil science and floristic inventories, have started to transform our understanding of plant exploitation, cultivation and domestication in tropical South America. Archaeobotanical studies are providing a far greater appreciation of the role of plants in the diets of early colonists. Since~13ka, these diets relied mainly on palm, tree fruits, and underground tubers, along with terrestrial and riverine faunal resources. Recent evidence indicates two areas of precocious plant cultivation and domestication: the sub-Andean montane forest of NW South America and the shrub savannahs and seasonal forests of SW Amazonia. In the latter area, thousands of anthropic keystone structures represented by forest islands show a significant human footprint in Amazonia from the start of the Holocene. While radiocarbon date databases show a decline in population during the middle Holocene, important developments happened during this epoch, including the domestication of cacao, the adoption of maize and the spread of manioc across the basin. The late Holocene witnessed the domestication of rice and the development of agricultural landscapes characterised by raised fields and Amazonian Dark Earths (ADEs). Our multi-proxy analysis of 23 late Holocene ADEs and two lakes from southern Amazonia provides the first direct evidence of field polyculture agriculture including the cultivation of maize, manioc, sweet potato, squash, arrowroot and leren within closed-canopy forest, as well as enrichment with palms, limited clearing for crop cultivation, and low-severity fire management. Collectively, the evidence shows that during the late Holocene Amazonian farmers engaged in intensive agriculture marked by the cultivation of both annual and perennial crops relying on organic amendments requiring soil preparation and maintenance. Our study has broader implications for sustainable Amazonian futures.