Olive mill wastewater (OMW) originating from a two-phase olive oil producing plant was treated with a crude polyphenol oxidase (PPO) homogenate, prepared from potato waste peels. The treatments carried out were based on a 2 3-full-factorial, central composite design (CCD) in order to identify optimal operational conditions with regard to polyethylene glycol (PEG) concentration, pH, and treatment duration. The treatment performance was assessed by estimating the % reduction in total polyphenol (TP) concentration. The model obtained produced a satisfactory fitting of the data (2 = 0.96, = 0.0017). The utilisation of the predictive model enabled the theoretical calculation of the optimal set of conditions, which were pH = 4, = 3.57 h, and [PEG] = 900 mg L −1. Under these conditions, the optimal theoretical % removal calculated was 54 ± 9. Examination of the treated samples with high-performance liquid chromatography (HPLC) showed that the potato homogenate afforded changes in the polyphenolic profile. Based on the experimental evidence, oxidation pathways were proposed.