This paper critically discusses the increasing trend in human microbiome research to draw on the concept of race. This refers to the attempt to investigate the microbial profile of certain social and ethnic groups as embodied racial traits. Here, race is treated as a necessary category that helps in identifying and solving health challenges, like obesity and type-2 diabetes, in ‘western’ or indigenous populations with particular microbial characteristics. We are skeptical of this new environmentalist trend to racialize human bodies due to two reasons: (i) These race studies repeat outdated historical narratives, which link especially nutrition and race in ways that are prone to stir stereotypical and exclusionary views on indigenous groups. (ii) The concept of biological race used here is taxonomically problematic and conceptually inconsistent. It leads to a view in which human races are constituted by other non-human species. In addition, this approach cannot group biological individuals into human races and decouples races from ancestry. To support this critique, we draw on case studies of microbiome research on indigenous groups in Latin America.