Widely applied pesticides have been detected in water bodies, which threatens the environment and non-target life. Thus, a promising treatment method, soybean peroxidase (SBP)-catalyzed process was studied to remove two halogenated benzonitrile pesticides Bromoxynil and Ioxynil through enzymatic oxidation from synthetic wastewater. SBP can be extracted from soybean hulls, a by-product of the soybean industry. First, the experiments studied the viability of SBP-catalyzed removal on these two compounds, then the operational parameters including pH, the molar ratio between hydrogen peroxide and substrate and minimum effective enzyme concentration were optimized. The first-order rate constant and half-life of each substrate were also determined under the established optimum conditions. The results demonstrated SBP is robust enzyme to achieve more than 95% removal efficiency for both compounds. In addition, the possible oligomeric products after enzymatic treatment were characterized by mass spectrometry and both dehalogenation and hydroxylation were observed after the reaction