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Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites for their effects on C. parvumgrowth in vitro. We identify eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6precursor, and indoles. Growth restriction of C. parvumby indoles does not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impairs host mitochondrial function and reduces total cellular ATP, as well as directly reducing the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delays life cycle progression of the parasite in vitro and reduces severity of C. parvuminfection in mice. Collectively, these findings indicate that microbiota metabolites impair mitochondrial function and contribute to colonization resistance to Cryptosporidiuminfection.