Recent research reveals that the increasing prevalence of food allergies (FA) is due in part to changes in the commensal microbiome. Studies in humans have shown that compared with healthy controls, individuals have distinct gut microbiomes during the onset and progression of FA. Mechanistic studies have established that the gut microbiota can affect the growth of immune tolerance to food antigens by modifying regulatory T cell differentiation, regulating basophil populations, and enhancing intestinal barrier function. New therapeutic and preventive approaches to altering the gut microbiota using diet adjustments, probiotics, prebiotics, synbiotics, postbiotics, fecal microbiota transplantation, and Chinese medicine have been developed towards FA. Herein, we summarized the latest evidence on the gut microbiota profiles and functions associated with FA, oral tolerance mechanisms, and gut microbiota-targeted therapeutic strategies for FA.