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Excess sludge minimization was studied in a MBR with pre-denitrification scheme. Sludge minimization, nitrogen removal performance and membrane fouling tendency were investigated in two configurations, characterized by a different position of the sludge retention reactor (SRR). In particular, the SRR was placed: i) in the return activated sludge line (Anaerobic Side-Stream Reactor – ASSR configuration) and ii) in the mainstream between the anoxic and aerobic reactor (Anaerobic Main-Stream Reactor – AMSR configuration). The achieved results demonstrated that the ASSR enabled a higher excess sludge reduction (74% vs 32%), while achieving lower biological nitrogen removal (BNR) (TN = 63% vs 78%) and membrane fouling tendency (FR = 2.1 · 1012 m−1 d−1 vs 4.0 · 1011 m−1 d−1) than the AMSR. It was found that metabolism uncoupling, destruction of EPS and endogenous decay simultaneously occurred in the ASSR. Conversely, selective enrichment of bacteria population with low biomass yield was found the main mechanism affecting sludge minimization in the AMSR.