Understanding the underlying mechanisms behind IgE-mediated cow’s milk allergy (IgE-CMA) is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies. Here, we report data on the gut microbiome, metabolome, and lipidome of 81 children affected by food allergies, including CMA and healthy controls. Moreover, we developed a mouse model that mimicked IgE CMA best, BALB/c mice sensitized with ß-lactoglobulin using cholera toxin. During sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid and tryptophan metabolites, that preceded allergic inflammation, while this inflammation was reflected in a disturbed sphingomyelin and histamine metabolism. We endorsed the microbial origin of these metabolites by in vitro colonic digestions and confirmed the microbial dysbiosis in our patient cohort, which was accompanied by metabolic signatures of low-grade inflammation. Our results suggest that gut dysbiosis precedes allergic inflammation, opening new opportunities for future prevention and treatment strategies. Trial: NCT04249973.