Seventeen pharmaceutically active compounds and 22 other trace organic pollutants were analysed regularly in the influent and permeate from a semi-real plant treating municipal wastewater. The plant was operated during 29 months with different configurations which basically differed in the type of biomass present in the system. These processes were the integrated fixed-film activated sludge membrane bioreactor (IFAS-MBR), which combined suspended and attached biomass, the moving bed membrane bioreactor (MBMBR) (only attached biomass) and the MBR (only suspended biomass). Moreover, removal rates were compared to those of the wastewater treatment plant (WWTP) operating nearby with conventional activated sludge treatment. Reverse osmosis (RO) was used after the pilot plant to improve removal rates. The highest elimination was found for the IFAS-MBR, especially for hormones (100% removal); this was attributed to the presence of biofilm, which may lead to different conditions (aerobic–anoxic–anaerobic) along its profile, which increases the degradation possibilities, and also to a higher sludge age of the biofilm, which allows complete acclimation to the contaminants. Operating conditions played an important role, high mixed liquor suspended solids (MLSS) and sludge retention time (SRT) being necessary to achieve these high removal rates. Although pharmaceuticals and linear alkylbenzene sulfonates showed high removal rates (65–100%), nonylphenols and phthalate could only be removed to 10–30%. RO significantly increased removal rates to 88% mean removal rate.