At the host-environment interface, the indigenous microbiome is poised to facilitate interactions with exogenous components. Here, we show that the microbiome is necessary for metabolic and transcriptional detoxification responses to the neurotoxic pyrethroid insecticide, deltamethrin. While oral deltamethrin exposure shapes gut microbiome composition, it is not directly microbially metabolized. Instead, we observe microbiome-dependence on host hepatic and intestinal detoxification responses, with diminished activity in germ-free mice. Colonization with a complex microbiome in adulthood maintained limited hepatic responses, suggesting developmental contributions. However, mono-colonization with specific microbes increased colonic expression of a key detoxification enzyme, revealing a protective role for active microbial signaling in the colon. Overall, our data demonstrate that the microbiome is necessary to prime and activate a host response against a model environmental toxicant. Through both developmental and active signaling across organ compartments, these data support that the microbiome may contribute to risk and outcomes of toxicant-associated disease.