The present study investigates the addition of several commercially available cationic (FO 4000 SSH and ADIFLOC series) and anionic (LT-25 Magnafloc) polyelectrolytes in a fully automated, pilot-scale Membrane Bioreactor (MBR), aiming to the development of an integrated methodology for the control of membrane fouling in MBR treatment systems. For this purpose, a series of batch experiments were conducted in order to evaluate their effectiveness on membrane fouling mitigation, using a typical hollow fiber, commercially available microfiltration membrane. Reversible fouling was assessed in terms of sludge filterability tests, whereas irreversible fouling was assessed in terms of SMPs (Soluble Microbial Products) concentration measurements. Results showed that the addition of cationic polyelectrolytes FO 4000 SSH series and ADIFLOC series were found capable to reduce both reversible and irreversible fouling. More specifically, the FO 4350 SSH type exhibited a remarkable performance, regarding both sludge filterability enhancement and SMP removal, when added at the concentration of 10 mg/L. Further comparison with the anionic polyelectrolyte LT-25 Magnafloc reinforced the allegation that cationic polyelectrolytes are preferable for control of membrane fouling, mainly due to charge neutralization mechanism.