Smallholder farming in Amazonia is practised mostly through shifting cultivation, which under low population pressure is well adapted to the low-fertility soils that predominate in uplands and to the lack of external inputs. In this paper we investigate the effects of soil heterogeneity (in terms of fertility and texture) on shifting cultivation systems in Central Amazonia. We focus on the effect of soil variation between anthropogenic upland soils (Amazonian Dark Earths, ADE) and surrounding soils on the size and location of cultivation plots, on the cultivation cycle, and on the diversity and assemblage of crops. We found that more fertile soils are cultivated more intensively (with shorter fallow periods, higher frequency of cultivation, shorter cycles and higher labour requirements) and with different crop assemblages, and have similar or larger numbers of crop species and/or landraces. Current smallholder farming systems along soil gradients between ADE and non-anthropogenic soils show that enhanced soil fertility can favour synergies between intensification and diversification in shifting cultivation.