Food allergy (FA) is an increasing public health concern, highlighting the urgent need for safe, bioactive-based preventive strategies. This study evaluated genistein, a plant-derived isoflavone, in an ovalbumin (OVA)-induced murine FA model. Genistein was administered before sensitization and throughout allergy induction. Clinical symptoms, rectal temperature, diarrhea, OVA-specific antibodies, mast cell responses, intestinal barrier markers, gut microbiota, short-chain fatty acids (SCFAs), and fecal metabolites were assessed using immunological, histological, microbiome, and metabolomic analyses. Genistein pretreatment prevented OVA-induced clinical symptom scores, rectal temperature decline, diarrhea occurrence, OVA-specific antibody responses, and mast cell responses. These changes were accompanied by preservation of jejunal tight junction-related markers and modulation of T-cell-associated immune responses. In vitro, genistein modulated antigen uptake, maturation-associated features of bone marrow-derived dendritic cells (BMDCs), and BMDC-driven CD4+ T-cell polarization. In parallel, genistein-pretreated mice showed altered gut microbial structure, higher relative abundances of selected SCFA-associated taxa, increased fecal butyrate, and fecal metabolomic alterations involving purine metabolism, bile-acid-related metabolism, and tryptophan-related microbial metabolites. Consistently, correlation analyses indicated associations among microbial taxa, metabolites, immune indicators, and intestinal barrier markers. Together, these findings provide preliminary mechanistic insight into genistein in experimental FA and support further investigation of genistein as a dietary bioactive candidate for FA prevention.