The objective of this study was to determine the effectiveness of anaerobic digestion in the treatment of polyphenols (PP) present in olive mill wastewater (OMW) and wine distillery wastewater (WDW). Anaerobic Toxicity Assay (ATA) was conducted to assess the impact of the most representative phenolic compounds present in OMW and WDW: catechol, tannins and p-Coumaric acid, on biogas production. The results from this study show that tannins do not present any inhibitory effect on methanogenesis at a concentration level of 1,664 ppm, whereas catechol has an inhibitory effect at 1,664 ppm. In addition, p-Coumaric acid was strongly inhibitory at 50 ppm. The co-digestion of OMW and WDW with other effluents was proposed as a solution for reducing the load of PP in the anaerobic medium. Biochemical methane potential (BMP) tests were carried out for dairy cattle manure and mixtures of five PP. A central composite design was implemented on the BMP tests to model the biogas production response and the degradation kinetics of PP. The co-digestion of WDW with cattle manure and/or whey was also investigated in BMP tests. The results show that the digestion was optimal at a ratio of 16: 64: 20 (WDW: manure: inoculum) with a maximum biogas yield of 172 mL/g of VS and 66% COD removal.