Debates about the relationship between racism, anti-racism, and the new life sciences calls for further inquiry into the growing popularity of microbiome science. Scientists define human microbiomes as unique communities of microorganisms that vary across body-sites, lifespan, location, and lifestyle. As new biomarkers for human diversity, scientists argue that microbiomes environmentally mediate development and health, which also reframes classical models of disease. In the small subset of literature that engages the stakes for race, the implications of human microbiome science are posed in terms of paradoxically reifying racism and empowering anti-racist science. To illustrate this duality, I first review the two most pervasive critiques of explicitly and implicitly reproducing racial categories in human microbiome science. Then, I show how some of the same critics embrace other versions of microbiome science as a tool to fight for environmental justice and de-essentialize race. However, in the next section, I challenge this distinction by arguing that even the most promising aspect of microbiome science as biosocial “becoming” can reproduce racial hierarchies too. In sketching limits in the current literature, I conclude by suggesting that critical engagements with biosocial formations of race need to further examine the relational formation of whiteness and that such inquiry requires elevating Black and Indigenous scholars.