Ongoing global climate change is affecting all aspects of life on Earth, including human health. The gut microbiota is an important determinant of health in humans and other organisms, but how climate change affects gut microbiota remains largely unexplored. In this Review, I discuss how the changing climate might affect gut microbiota by altering the quantity and quality of food, as well as environmental microbiomes, such as enteric pathogen pressure and host physiology. Climate change-induced variability in food supply, shifts in elemental and macromolecular composition of plant and animal food, the proliferation of enteric pathogens, and the direct effects of high temperatures on gut physiology might alter gut microbiota in undesirable ways, increasing the health burden of climate change. The importance of different pathways might depend on many geographical, economic, and ecological factors. Microbiomes of populations in low-income countries might be disproportionally affected through greater climate change effects and poor mitigation on diet, pathogen burden, and host physiology.