Studies on pre-Hispanic populations in the Amazon region are rare and mostly focus on the remains of the earliest humans in the region. There is currently a complete lack of relevant studies for the southwest of Amazonia. In this paper we present the results of a comprehensive multi-disciplinary study on the skeletal remains of 125 individuals from the pre-Hispanic Casarabe culture settlement Salvatierra. The Casarabe culture flourished between 500–1400 AD in the southeast of the Llanos de Mojos, which make up a large part of the Amazon lowlands of Bolivia. The study, conducted in 2007 and 2008, involved classic osteological examinations, as well as analyses of ancient DNA, isotopes, and trace elements.