AbstractThe purpose of this research was to investigate the effect of bioactive peptides isolated from soy whey on the physicochemical, sensory, and microbiological characteristics of yogurt during storage. Trypsin was utilized to hydrolyze soy whey protein at 45°C for 4 h. Then, the resulting protein hydrolysate was fractionated using reversed phase‐high performance liquid chromatography (RP‐HPLC). Since the F7 fraction showed the best antioxidant and antibacterial capabilities, different levels (6.5, 13, and 17 mg/mL) of this peptide fraction were added to yogurt. A control sample (without the bioactive peptide) was also prepared. Yogurt samples were stored for 3 weeks. With the increase in peptide concentration, the antioxidant activity of yogurt increased while viscosity and syneresis decreased (p< .05). During storage, yogurt acidity, syneresis, and viscosity increased while pH and antioxidant activity declined (p< .05). The addition of bioactive peptide reduced the quantity ofEscherichia coliandStaphylococcus aureusbacteria in yogurt during storage (p< .05), and the reduction in bacterial quantity was stronger as the peptide content was increased. The sample containing the largest concentration of peptide (17 mg/mL) got the lowest overall acceptability score. The level of 13 mg/mL of the peptide was chosen as the best concentration for yogurt fortification in terms of overall acceptance and functional properties. Therefore, soy whey‐derived peptide can be utilized as a functional component as well as a natural preservative in yogurt.