The combination of a laccase–hydroxybenzotriazole (HBT) mediator system with/without cellobiose dehydrogenase (CDH) or an additional Fenton reaction step for the elimination and/or detoxification of phenolic compounds in dry olive mill residues (DOR) and liquid olive mill wastewaters (OMW) was evaluated. The laccase–HBT–CDH and laccase–HBT–CDH–Fenton system were the most effective, removing at least 69 and 72 % of phenolic compounds from a total of 698 and 683 mg in OMW and DOR, respectively, in 12 h. The efficient removal of phenolic compounds was also accompanied by >80 % reduction in biochemical oxygen demand and chemical oxygen demand in both DOR and OMW. Microbial community analysis using single-strand conformation polymorphism (SSCP) gels showed that biogas reactors supplemented with untreated and laccase–HBT–CDH–Fenton-treated DOR and OMW strongly inhibited growth of microorganisms. In contrast, the laccase–HBT- and laccase–HBT–CDH-pretreated OMW and DOR were detoxified as evidenced by SSCP analysis, which also indicated a distinct sensitivity of the individual members of the anaerobic population toward the toxicants. Further, although the laccase–HBT–CDH–Fenton system was effective in bleaching and removing phenolic compounds in both OMW and DOR, it was not able to support methane production. However, laccase–HBT and laccase–HBT–CDH indeed supported biogas production. This study therefore shows that the laccase–HBT–CDH system has a potential for the detoxification of olive mill residues, which can be potentially used as substrates for downstream processes.