► MBR process is more effective than CASP in the removal of bacteriophages. ► SOMCPH proves to be more resistant to MBR treatment than FRNAPH. ► BFRAGPH are not always detectable in the pre-treated effluent. ► SOMCPH are the most suitable indicators to evaluate the MBR process performance. ► SOMCPH are the most suitable indicators to evaluate the safety of the MBR effluent. The effectiveness of a full scale membrane bioreactor (MBR) in the removal of bacteriophages and bacterial fecal indicators from municipal wastewater was compared with that obtained by conventional activated sludge process (CASP). Somatic coliphages (SOMCPH) and F-RNA specific bacteriophages (FRNAPH) were always detected in the pre-treated effluent (mean: 6Log10), while phages infecting Bacteroides fragilis were not always present (mean: 3.9Log10). The MBR process was able to achieve respectively 2.7 and 1.7Log10 higher reductions of SOMCPH and FRNAPH compared to CASP (significant differences: P<0.05). SOMCPH were found to be the most suitable indicators for assessing MBR performance, since they showed greater resistance to biofiltration than FRNAPH and a more regular distribution in pre-treated effluent than BFRAGPH. Moreover, since the traditional bacterial indicators were almost totally removed by biofiltration, SOMCPH proved to be the best indicators to evaluate the microbiological risk when MBR effluent is discharged into natural waters or reused.