Soybean Trypsin Inhibitors (STIs) in soy-based foods have negative effects on soybean protein digestion and pancreatic health of humans. The inactivation of STIs is a critical unit operation aimed at enhancing the nutritional properties of soy-based foods during processing. This paper reviews the structure of STIs and soybean proteins, as well as the mechanisms of digestion. Various technologies (physical, chemical, biological) have been used to inactivate STIs. Their parameter settings, operating procedures, advantages, and disadvantages are also described. Mechanisms of inactivation of STIs (Kunitz trypsin inhibitor (KTI) and Bowman–Birk inhibitor (BBI)) conformations under different treatments are clarified. In addition, emerging technologies, e.g., Ohmic Heating, Electron Beam Irradiation, Dielectric-Barrier Discharge, and probiotics, have demonstrated great potential to inactivate STIs. We advise that multiple emerging technologies should combine with other unit operating systems to maximize inactivation efficiency.