Bleached kraft mill requires large quantities of water and chemicals reactives and generates effluents containing active organic compounds. Specifically, hormonal changes in fish and their communities have been demonstrated, which could be attributed to endocrine-disrupting chemicals (EDCs) contained in kraft mill effluents. This chronic toxicity is attributable to extractive compounds, such as resin acids, sterols, and fatty acids. The goal of this work is to evaluate the methanogenic toxicity and anaerobic biodegradation of stigmasterol and beta-sitosterol. A continuously anaerobic filter (AF) was used for the anaerobic biodegradation of stigmasterol and beta-sitosterol. Three phases were evaluated. In phase I, an elementary chlorine-free bleached kraft mill effluent was fed to the reactor whereas in phases II and III, the effluent was supplemented with increasing stigmasterol and beta-sitosterol concentrations. The AF displays high performance in biological oxygen demand (BOD5) removal (up to 94%); however, only 50% of the chemical oxygen demand (COD) was removed. Simultaneously, the AF system shows a great ability to remove beta-sitosterols (77-100%) and stigmasterols (87-95%). No negative effect on the methanogenic activity inhibition was shown by beta-sitoesterols and stigmasterol. However, a mixture of beta-sitosterols and stigmasterols (ratio 1 : 1) caused a less than 10% reduction in methanogenic activity.