High levels of peptides can accumulate in tissues of legumes during germination. In this study, effects of germination conditions (pH, temperature, and time) on protease activity and peptides accumulation in soybean were investigated. The desirable level scope of parameters was used to further optimise germination conditions for peptides accumulation using response surface methodology. Results showed that protease activity and peptides yield were significantly influenced by pH, temperature, and time (P<0.05). The optimal pH, temperature, and time for protease activity were 5, 25 °C, and 6 days, respectively. Meanwhile, the optimal pH, temperature, and time for peptides content were 5, 30 °C, and 5 days, respectively. Box–Behnken design indicated the following optimal germination conditions: pH 4.8, temperature 29 °C, and time 5 days. Under these conditions, the highest peptides content (14.46 mg g–1 FW) in germinated soybean was obtained. The present study indicates that germinated soybean can be a valuable component of peptides-enriched foods.