The highly fertile Amazonian Dark Earths (ADE) results from landscape transformations found in association with archaeological sites throughout Amazonia. In the Lower Tapajos region, ADEs are found in ancient Tapajó settlements dated to the Late Pre-Columbian period (AD 1000-1600). This research focuses on plant management associated with the regional formation of ADE. Three ADE sites are analysed for microbotanical remains. Phytolith and microcharcoal (< 125μm) from test pits and excavation profiles reveal diverse plant-use including food and non-food plants. Geochemical data indicated a variety of formations processes intra-site. The inter-site comparison indicated a gradiente of vegetation change related with the formation of ADEs. Aditionally, small changes folloed the adoption of cultigens together with ADE formation. These data suggest the practice of polyculture agroforestry in the investigated sites.