Soybean production and consumption has increased in recent decades. However, trypsin inhibitor activity and “beany” flavour are two drawbacks limiting the utilization of soybean. In the present study, micronization, ethanol washing, and enzymatic hydrolysis (alone or in combination) were used to treat soybean. Micronization at 100 °C and 135 °C decreased the activity of both trypsin inhibitors (53% and 80% respectively), and lipoxygenase (51% and 99%, respectively). Ethanol increased the trypsin inhibitor activity while alcalase hydrolysis decreased its activity. Different treatment combinations affected trypsin inhibitor activity, with micronization having a major influence. “Beany” flavour related volatiles (hexanal, (E)- 2-hexenal, 1-hexanol, heptanal, (E)-2-octenal, (E)-2-nonenal, (E,E)-2,4-nonadienal, 2,4-decadienal, (E,E)-2,4-decadienal, 1-octen-3-ol, 2-pentylfuran and 3-octen-2-one) were significantly decreased with micronization. Ethanol effects varied with different volatiles. Soybean micronized at 135°C and washed with 65% ethanol was recommended for soybean processing due to its low trypsin inhibitor activity and low “beany” related volatile content.