Stigmasterol is a phytosterol contained in kraft mill effluent that is able to increase over 100% after aerobic biological treatment. This compound can act as an endocrine disrupter as its structure is similar to that of cholesterol. Furthermore, stigmasterol contained in kraft mill effluent shows high toxicity (25-fold more than β-sitosterol) to aquatic organisms such as Daphnia magna. However, the operation of the aerobic treatment and biomass adaptation could be affecting their removal. The performances of activated sludge (AS), aerated lagoon (AL), and moving bed biofilm reactors (MBBR) are compared to remove the stigmasterol contained in kraft mill effluent. The AL operates at a hydraulic retention time of 6 h and removes up to 90% of phytosterols. So, a 96% of stigmasterol is removed by AL when the sterol retention load is 0.6 mg/L · d. However, stigmasterol concentrations increase from 29% to 37% at a low stigmasterol load rate (0.2 mg/L · d). On the other hand, the stigmasterol is removed between 65% and 87% by an AS under a hydraulic retention time of 3 h. Moreover, a 100% of stigmasterol can be removed by the MBBR when the hydraulic retention time is 2 days.