Olive mill waste water (OMWW) originating from a two-phase olive oil-producing plant was treated with a crude peroxidase extract prepared from onion solid by-products. The treatments were based on a 3 9 3 factorial design, employing a series of combinations of pH and H 2 O 2 , in order to identify optimal operational conditions. The treatment performance was assessed by estimating the removal percentage of total polyphenols. The model established produced a satisfactory fitting of the data (R 2 = 0.94, p = 0.0158), while the second-order polynomial equation used to describe the process indicated that peroxidase-catalysed polyphenol removal in diluted OMWW is facilitated at relatively low pH and intermediate H 2 O 2 values. A predicted value of 50.7 ± 9.5% removal was calculated under optimal operational conditions (pH 2.76, [H 2 O 2 ] = 3.56 mM). Analysis of an untreated and an optimally treated sample by high performance liquid chromatography revealed that enzyme treatment brought about alteration in the original OMWW polyphenolic profile. The use of peroxidase from onion solid by-products is proposed as an alternative means that could have a prospect in bioremediation applications.