The Amazon witnessed the emergence of complex societies after 2500 years ago that altered tropical landscapes through intensive agriculture and managed aquatic systems. However, very little is known about the context and conditions that preceded these social and environmental transformations. Here, we demonstrate that forest islands in the Llanos de Moxos of southwestern Amazonia contain human burials and represent the earliest settlements in the region between 10,600 and 4000 years ago. These archaeological sites and their contents represent the earliest evidence of communities that experienced conditions conducive to engaging with food production such as environmental stability, resource disturbance, and increased territoriality in the Amazonian tropical lowlands.