Soybean β-conglycinin (7S) is a major food allergen, and mitigating its allergenicity is critical for food safety. In this study, the potential of glycitein (Gly), a dietary isoflavone, to modulate 7S allergenicity was evaluated. Spectroscopic and molecular-simulation analyses revealed that Gly bound to 7S mainly through hydrogen bonding and van der Waals forces, loosening its conformation to enhance protease accessibility and digestibility. In vitro, Gly moderately reduced IgE binding and significantly decreased β-hexosaminidase and IL-6 release. In vivo, it showed that allergic reactions were weakened, with lower antibody levels in serum and significant suppression of IL-4 in spleen. Gly also partially restored Th1/Th2 balance and modulated gut microbiota composition by normalizing the ratio of Firmicutes/Bacteroidetes while enriching beneficial genera such as Faecalibacterium. Overall, Gly mitigated 7S allergenicity through structural remodeling, enhanced digestibility, and immune-microbiota modulation, highlighting its potential as a functional ingredient for hypoallergenic soy-based foods.