A direct comparison between parallel activated sludge and integrated fixed-film activated sludge (IFAS) processes was performed in this study because both treatments received the same primary effluent, although differences may still remain due to different return flow rates. Modern ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry was applied to characterize the complexity of effluent organic matter (EfOM) and to evaluate both processes in their abilities to change the EfOM molecular composition. At different stages during the two processes a direct comparison of the performance and changes in molecular composition of the IFAS with those of the activated sludge was undertaken. Large differences in the molecular composition between both processes were only apparent in the early stage of the aeration cells and the first cell of the IFAS possibly due to the higher flow rate and a delay in aerobic bacterial degradation. Despite the double flow rate (0.263 m(3) s(-1)) in the IFAS reactors compared to the activated sludge, by the end of the treatment the EfOM composition of both processes were undistinguishable from each other. However, a much more complex EfOM was generated in both processes, suggesting that bacteria are responsible for an increase in molecular diversity in the effluent.