The objective of this study was to determine the effect of advanced oxidation process with the use of Fenton’s reaction on the effectiveness of anaerobic treatment of wastewaters originating from the wood industry that were characterized by a high concentration of formaldehyde. Experiments were established to analyze changes in COD content and in the concentration of formaldehyde in treated wastewaters, additional analyses were carried out to assay quantitative and qualitative changes in the biogas produced. The first stage of the experiment involved analyses of the effectiveness of the tested wastewaters treatment only in the process of methane fermentation. At the second stage of the experiment, the biological process was preceded by chemical pre-treatment of wastewaters with Fenton’s reagent. The conducted study proved that the investigated variants of chemical pre-treatment of wastewaters had a significant effect on increasing the total biogas production. In contrast, no significant effect of the applied technology was demonstrated on changes in the concentration of the analyzed contaminants in the treated wastewaters.