Soybean is widely used as a protein source in human and animal nutrition because of its high protein and oil contents. However, antinutritional factors, mainly lectin and Kunitz and Bowman-Birk protease inhibitors impair the nutritional value of this protein source. The goal of the current study was to evaluate the centesimal composition, trypsin inhibition, urease and hemagglutinating activities of conventional (CSB) and lectin and Kunitz free (KFLF) soybean flours. The soybean flours were autoclaved for 0, 5, 10, 15 and 25 minutes. After the 25 min heating period, the urease activity values decreased from 1.85 to 0.02 DpH for CSB and from 1.91 to 0.08 DpH for KFLF. The trypsin inhibition decreased from 40.75 to 1.09 mg of inhibited trypsin per gram of protein for CSB and from 27.62 to 0.34 for KFLF. The same treatment caused a reduction on hemagglutinating activity from 1.28 to 0 mg/mL for CSB. In the case of KFLF, hemagglutinating activity was absent even before the heat treatment.  The centesimal composition determination demonstrated that the breeding process by which KFLF soybean was created significantly reduced trypsin inhibition and removed lectin, but maintained the protein and oil contents. The simultaneous reduction of urease activity and trypsin inhibition in both soybean flours after the heating treatment confirmed that urease activity is a good indicator of trypsin inhibition. As for lectin, it was completely inactivated after the 25-min heating treatment, demonstrating that this protein is more heat-sensitive than the Kunitz inhibitor.