SummaryThis study delved into the antimicrobial potential of hydrolysates from adzuki bean and mung bean protein concentrates, created using Alcalase and Flavourzyme enzymes. Targeting common foodborne pathogens (Salmonella Typhimurium, Salmonella Enteritidis, Vibrio parahaemolyticus, Staphylococcus aureus, and Bacillus subtilis) and Escherichia coli, the research underscored the crucial role of peptidase in generating antibacterial peptides. Fractions F2 of Flavourzyme hydrolysed adzuki bean (ABF) and F4 of Flavourzyme hydrolysed mung bean (MBF) showed the highest antibacterial activity against S. Typhimurium and S. aureus, respectively, whereas F2 of Alcalase hydrolysed mung bean (MBA) exhibited very poor activity against S. aureus. TripleTOF LC–MS/MS analysis revealed small cationic antibacterial peptides, with lysine being prominent against S. aureus and proline–proline against S. Typhimurium. These findings highlighted the significant contribution of protease enzymes in fostering antibacterial peptide production, offering valuable insights for developing effective antimicrobial agents in the context of food safety.