Evidence from several earthwork-building societies has recently been discovered in Amazonia that challenges existing theories about precolonial, human-environment interactions. Combining data obtained by plant macrofossil analyses, archaeological excavations, historical sources, and indigenous oral histories, we focus on the pre-colonial sources of subsistence and domestication processes of some tree species. Our study shows that the societies that built geoglyph-type earthworks in southwestern Amazonia harvested and consumed both wild and domesticated palm fruits, Brazil nuts and other identified species in the first millennium of the Common Era. Drawing on theories of human ecology, we argue that in the pre-colonial Amazonian context, plant domestication occurred as complex and nonlinear activities of protecting, supporting, and cultivating. This multifaceted indigenous cultural phenomenon of domestication had an important long lasting impact on Amazonian forest composition, and it is obvious that human and botanical interaction has also led to clear and observable differences in Brazil nuts and some palm fruits compared to their ancestors.