Raw soybeans are not suitable for consumption due to their high levels of anti-nutritional factors, such as trypsin inhibitors (TIs). The two main TIs in soybean, the Kunitz trypsin inhibitor (KTI) and the Bowman-Birk trypsin inhibitor (BBTI), were isolated to evaluate the impact of meal processing on their binding affinities for animal serine proteases. BBTI showed a ∼10fold stronger affinity for trypsin compared to KTI, whereas KTI showed a ∼40-fold stronger affinity for chymotrypsin than BBTI. No correlation was observed between the TI concentration in soybean meal and affinity for trypsin. Further analysis using mass spectrometry and protein sequence identified distinct reactive site loops for protease binding in BBTI and KTI variants, which were associated with their binding affinities for specific serine proteases. Our findings indicate that KTI and BBTI have a preference when interacting with specific animal serine proteases, suggesting that both inhibitors are equally important when considering the nutritional quality of soybean meal, regardless of their concentration.