Bowman-Birk Inhibitors (BBIs) are plant-derived serine protease inhibitors with diverse biological activities and significant therapeutic potential. Originally isolated from soybeans, BBIs have demonstrated potent anticancer effects that surpass those of other soy-derived agents. This review comprehensively examines the multifaceted therapeutic applications of BBIs, including their anticancer, anti-inflammatory, antimicrobial, and gastrointestinal protective properties. We explore the structural and stability features and evolutionary relationships that underpin BBIs’ unique dual-inhibitory activity against serine proteases. The molecular mechanisms through which BBIs exert their effects—such as modulation of key signaling pathways, immune regulation, and microbial membrane disruption—are also discussed. Advances in synthetic peptide mimics, exemplified by sunflower trypsin inhibitor-1 (SFTI-1), highlight opportunities for therapeutic optimization. Additionally, clinical trial data on Bowman-Birk Inhibitor Concentrate (BBIC), a BBI-enriched soybean extract, demonstrate safety and efficacy without neutralizing antibody development. This review synthesizes current insights into BBIs, underscoring their remarkable versatility and promising role in cancer prevention, inflammatory disease management, and antimicrobial therapy, while addressing ongoing challenges and future directions.