We all do things that impact our own microbiomes in ways that can be beneficial and detrimental to our health. However, many of the forces that shape microbiomes and their effects from ecosystems to populations to individuals are outside our personal control. Microbiome stewardship comprises the collective efforts we must make through policy and action to protect the microbiomes that benefit humans and their environment, and impede the microorganisms and microbial communities that can cause us harm. The Microbiome Stewardship initiative aims to define core principles, policies, and collective actions that can protect the vital and often underappreciated microorganisms that shape our health and that of the world around us.