Because of the health benefits and economic opportunities, extracting bioactive peptides from plant proteins, often food processing by-products, garners significant interest. However, the high enzyme costs and the emergence of bitter peptides have posed significant challenges in production. This study achieved the immobilization of Alcalase and Flavorzyme using cost-effective SiO₂ microparticles. Mussel-inspired chemistry and biocompatible polymers were employed, with genipin replacing glutaraldehyde for safer crosslinking. This approach yielded an enzyme loading capacity of approximately 25 mg/g support, with specific activity levels reaching around 180 U/mg for immobilized Alcalase (IA) and 35 U/mg for immobilized Flavorzyme (IF). These immobilized proteases exhibited improved activity and stability across a broader pH and temperature range. During the hydrolysis of soy proteins, the use of immobilized proteases avoided the thermal inactivation step, resulting in fewer peptide aggregates. Moreover, this study applied peptidomics and bioinformatics to profile peptides in each hydrolysate and identify bioactive ones. Cascade hydrolysis with IA and IF reduced the presence of bitter peptides by approximately 20%. Additionally, 50% of the identified peptides were predicted to have bioactive properties after in silico digestion simulation. This work offers a cost-effective way of generating bioactive peptides from soy proteins with reducing potential bitterness.