The Kunitz trypsin inhibitor (KTI) and the Bowman−Birk inhibitor (BBI) of trypsin and chymotrypsin contain disulfide bonds. Glycinin, the major storage protein in soybeans also contains disulfide bonds. Treatment of soy white flour with a NADP−thioredoxin system (NTS) effectively reduced disulfide bonds in soy flour and increased protein digestibility by trypsin and pancreatin as measured by the pH stat method. Treatment of soy flour with NTS increased the digestibility compared to soy white flour by 29.3 and 60.6% for trypsin and pancreatin, respectively. NTS-treated soy flour had similar digestibility by trypsin to autoclaved soy flour and casein, but digestibility by pancreatin was less than autoclaved soy flour and casein. The degree of reduction by NTS was highly correlated to the degree of hydrolysis (DH) by trypsin (R² = 0.93) and pancreatin (R² = 0.99). The DH of NTS-treated soy flour by trypsin is reflective of both inactivation of trypsin inhibitors and overall protein digestibility while pancreatin hydrolysis is reflective of only overall protein digestibility.