Protein digestibility of soybean (soaked "S", boiled "B", and fermented "F" soybeans) was changed as 20.58 ± 0.25%, 48.71 ± 0.04%, and 50.21 ± 0.45%, respectively in the preparation of soybean fermentation. After simulated digestion, the increment rate of protein digestibility of both B and F was comparable and higher than that of S accompanying by the accumulations of small protein sub-fractions and essential amino acids. Interestingly, bioactivity parameters of all digested fractions increased by around 2 to 4-fold when digestion stages were progressed with overall F showed the maximum values. Processing not only improves the palatability but also increases protein utilization, the bioavailability of nutrients, and healthy support. The study verified the effect of processing and the benefits of soybean and fermented soybean beyond their basic nutrients which could be claimed as functional foods with higher protein digestibility and indispensable amino acids as well as potential bioactivities.