The aim of this article was to treat olive oil mill waste with onion peroxidase with regard to the removal of polyphenols and decolonization. Determination of the optimum conditions for the treatment of olive mill wastewater was another objective of this study. Results showed a pH optimum of around 2.65 and a concentration of H2O2 of around 2.58 mM. Moreover, o-diphenols could be removed in a short period of time in comparison to the total phenols. The results showed that three hours were sufficient for 75% removal of o-diphenols. Dilution 1 over 20 of the olive mill wastewaters and the addition of some additives (NaCl and polyethylene glycol) in the treatment of olive mill wastewater (OMW) could enhance the efficiency of total phenol removal as well as, a decrease in the color intensity of the olive oil wastewater. In addition, high performance liquid chromatography (HPLC) analyzes were carried out on samples representing OMW before and after the treatment. Results showed that the degradation of some phenols was carried out with the use of onion peroxidase, as well as with the use of the optimal conditions regarding the pH and the concentration of hydrogen peroxide. It was concluded that onion peroxidase could catalyze the degradation of total phenols and o-diphenols and that such degradation could also influence the change in color and the antioxidant activity of the olive oil mill wastewater.