The soybean is a protein source of high biological value. However, the presence of anti-nutritional factors affects its protein quality and limits the bioavailability of other nutrients. The effect of heat-treatment, 150 ºC for 30 minutes, on hulled and hull-less soybean flour from the cultivar UFVTN 105AP on urease, trypsin inhibitor activity, protein solubility, amino acid profile, and in vivo protein quality was investigated. The treatment reduced the trypsin inhibitor activity and urease, but it did not affect protein solubility. Protein Efficiency Coefficient (PER) values of the flours were similar, and the PER of the hull-less soybean flour did not differ from casein. The Net Protein Ratio (NPR) did not differ between the experimental groups. The True Digestibility (TD) of the flours did not differ, but both were lower in casein and the Protein Digestibility Corrected Amino Acid Score (PDCCAS) was lower than the TD, due to limited valine determined by the chemical score. Therefore, the flours showed reduced anti-nutritional phytochemicals and similar protein quality, and therefore the whole flours can be used as a source of high quality protein.