A membrane bioreactor (MBR), a hybrid moving-bed biofilm reactor-membrane bioreactor (hybrid MBBR-MBRa) containing carriers in the anoxic and aerobic compartments, and a hybrid MBBR-MBRb containing carriers only in the aerobic zone were used in parallel and compared for treating municipal wastewater. The microbial kinetics and the evolution of the enzymatic activities of alpha-glucosidase and acid and alkaline phosphatase as well as the bacterial diversity and bacterial community structure were studied to explain the removal of organic matter and nutrients. The MBR and the hybrid MBBR-MBRb showed the highest reduction percentages of chemical oxygen demand. Moreover, the hybrid MBBR-MBRb exhibited the highest removal performance of total nitrogen.