Climate change, biodiversity loss, and antimicrobial pollution caused by human activity are placing pressure on global microbiota. However, microbial protection remains mostly absent from international law and global governance frameworks. This policy brief highlights the chronic marginalisation of microbes in international health, environmental, and human rights law, as well as in governance frameworks addressing antimicrobial resistance (AMR). Drawing on recent genomics and humanities research, it argues that policymakers need to abandon interventions designed to control or combat individual microbes in favour of microbiota-oriented governance. This brief discusses three major areas (pollution thresholds, microbial conservation, and the human right to a clean, healthy, and sustainable environment) where change is already occurring.