Purpose of review The rise in the prevalence of food allergy over the past decades has focused attention of factors that may impact disease development, most notably the gut microbiota. The gut microbial communities play a crucial role in promoting oral tolerance. Their alteration by such factors as Cesarean section delivery, diet and antibiotics may influence disease development. This review highlights recent progress in our understanding of the role of the gut microbiota in the development of food allergy. Recent findings Food allergy is associated with alterations in the gut microbiota or dysbiosis early in life that may be predictive of disease persistence versus tolerance acquisition. Evidence for the benefits of adjunct therapy with probiotics for the prevention of food allergies and for potentiating oral immunotherapy remains circumstantial, with further studies needed to validate its use. Studies in murine models of food allergy suggest that microbial therapy with protolerogenic bacteria such as certain Clostridial species holds promise in future applications for prevention or therapy of food allergy. Summary Progress in understanding the role of dysbiosis in food allergy and the factors that promote its development, such as antibiotic therapy, diet, modes of infant delivery, and environmental exposures, offer windows of opportunity for both preventive and therapeutic interventions to stem the rising tide of the food allergy epidemic.