The increasing prevalence of allergic diseases, particularly in industrialised populations, has intensified interest in environmental factors that shape immune homeostasis. Among these, disturbances in the gut microbiota (dysbiosis) have been increasingly recognised as important contributors to immune dysregulation and allergy development. Growing evidence indicates that microbiota-derived metabolites play a central role in the microbiota–immune system axis, acting as key mediators between intestinal microorganisms and host immunity.

This review examines the mechanisms through which microbial metabolites influence the development and modulation of allergic diseases and evaluates their therapeutic potential. Particular attention is given to short-chain fatty acids (SCFAs), tryptophan-derived metabolites, and secondary bile acids. SCFAs, including acetate, propionate, and butyrate, promote regulatory T-cell differentiation, suppress Th2-skewed inflammatory responses, and enhance epithelial barrier integrity through activation of GPR41/43 receptors and inhibition of histone deacetylases (HDACs). Tryptophan metabolites acting via the aryl hydrocarbon receptor (AhR) support mucosal immunity, tissue repair, and maintenance of intestinal barrier function, whereas secondary bile acids regulate inflammatory signalling and Treg/Th17 balance through FXR and TGR5 pathways. Disturbances in these metabolic pathways have been associated with asthma, food allergy, and atopic dermatitis. Although clinical translation remains at an early stage, microbiota-derived metabolites represent promising biomarkers and therapeutic targets in precision allergy medicine. Further mechanistic and interventional studies are required to facilitate their integration into future preventive and therapeutic strategies.