The main objective of this study was to eliminate the hemagglutination activity of an antinutritional factor in soybeans, soybean agglutinin (SBA). A series of experiments was designed to enzymatically modify SBA structure and to use other physical treatments to reduce activity. SBA extract was prepared from soy flour and used as the substrate for all treatments. Deglycosylation by enzyme decreased activity of SBA by 21%, but not to the level of denaturation by heat or by denaturing reagents (47−77% residual activity). Single enzymes, such as trypsin, chymotrypsin, thermolysin, and endoproteinase Glu-C, did not hydrolyze native SBA, but they hydrolyzed heat- or organic solute-denatured SBA. Even after hydrolysis, SBA still had 44−62% residual activity. Combinations of enzymes with thermolysin fully deactivated heat- or guanidine hydrochloride- and urea-treated SBA. Pepsin and pancreatin hydrolysis fully deactivated not only heated but also native SBA. Tea polyphenols, metal ions, and chelating agents were also tested, and they showed no significant effect on SBA activity. N-Acetylgalactosamine−agarose beads specifically but not fully removed SBA from the soy protein mixture. In general, SBA needs to be denatured first for an effective enzymatic hydrolysis, and multiple enzymes are needed to fully deactivate SBA. Pepsin and pancreatin treatment showed great promise in fully reducing SBA activity, and it would be further tested using soy flour as a model system.