The global prevalence of atopic diseases, including food allergy, is increasing and correlates with shifts in the commensal microbiota triggered by modern lifestyle factors. Current research focuses on the immunological mechanisms and microbial cues that regulate mucosal immunity and prevent allergic responses to food. We review the identification and characterization of novel antigen-presenting cell subsets that may be critical for the establishment and maintenance of tolerance to both food and intestinal bacteria. Microbially derived products, particularly from the Lachnospiraceae family of Clostridia, regulate intestinal homeostasis through a variety of mechanisms. Here, we highlight recent work on Clostridial metabolites and products that mediate protection against allergic responses to food.