Membrane separation technologies equipped with ceramic membranes have shown good operational results and high robustness and reliability. In this study, a combination of Moving Bed Biofilm Reactor (MBBR) & Membrane Bioreactor (MBR) (pilot scale) was investigated for fouling control optimisation. The system was operated with flat-sheet microfiltration (MF) ceramic membranes. Because of the attached biofilm in the MBBR, it could work stably and effectively with different loading rates, which reduces the load on the membrane surface. Influences of sludge recirculation and flux on the transmembrane pressure (TMP) value and thus impact on fouling development were investigated. Intensive aeration, backwash as well as the implementation of NaOCl were used respectively as physical and chemical cleaning. Chemical cleaning efficiency reaches up to 70% and could be increased after further research. After the determination of optimal operational conditions, the normalised permeability value (PN) was effectively maintained with a slight TMP increase.