Soybean has a high biological value because it is a potential nutraceutical that benefits human health. Isolated peptides of soybean have been associated with activities such as anticancer, antioxidants, antiobesity, antithrombotics, hypocholesterolemic, antidiabetic, immunomodulatory and antimicrobial, and this last activity is also obtained from microorganisms isolated from soybean subjected to processes such as fermentation, which can act directly against pathogens that are resistant to antibiotics or participate in the synthesis of new peptides with antimicrobial activity, so they could be used as preservatives in food as an alternative in the prevention of diseases. Strains of Bacillus subtilis isolated from soybean are mainly those that have the ability to inhibit the growth and proliferation of pathogens; some fungi such as Rhizopus microspores and Aspergillus oryzae have also had an inhibitory effect. This chapter describes the potential of microorganisms and peptides obtained from different sources of soybean against pathogenic microorganisms responsible for foodborne diseases.

Whey is a major by-product of the dairy industry and represents a valuable source of proteins that can be enzymatically converted into bioactive peptides with diverse health-related functions. In recent years, increasing attention has been given to whey-derived peptides due to their antioxidant, antihypertensive, antimicrobial, anti-inflammatory, antithrombotic, immunomodulatory, and anticancer activities, highlighting their potential use as functional ingredients and nutraceutical compounds. The generation and biological functionality of these peptides are strongly influenced by the protein source, processing conditions, enzymatic or microbial hydrolysis strategies, and peptide structure. Unlike the existing literature, this review provides an analysis of individual peptide sequences, meticulously linking their specific chemical structures to their diverse biological activities, such as antioxidants, antihypertensive, and immunomodulatory effects. By moving beyond general protein hydrolysis, this work offers a unique comparative framework that evaluates how these distinct peptide fractions perform under industrial conditions. Furthermore, it bridges the gap between laboratory discovery and commercial implementation, focusing on critical parameters for large-scale production, stability in functional food matrices, and the regulatory pathways required for market-ready nutraceuticals. This integrated approach provides a strategic roadmap for translating molecular bioactivity into high-value industrial applications. This review provides an applied overview of recent advances in the production of whey bioactive peptides, emphasizing enzymatic generation methods, structure–activity relationships, and underlying mechanisms of action associated with their biological effects. In addition, current and emerging applications of whey-derived peptides in functional foods, nutraceuticals, and health-oriented formulations are critically discussed. Finally, key challenges related to peptide stability, bioavailability, industrial scalability, and regulatory aspects are addressed to identify future perspectives for the effective translation of whey bioactive peptides from research to practical applications.