The main aim of this study was to develop an advanced controller to optimise filtration in submerged anaerobic MBRs (SAnMBRs). The proposed controller was developed, calibrated and validated in a SAnMBR demonstration plant fitted with industrial-scale hollow-fibre membranes with variable influent flow and load. This 2-layer control system is designed for membranes operating sub-critically and features a lower layer (on/off and PID controllers) and an upper layer (knowledge-based controller). The upper layer consists of a MIMO (multiple-input-multiple-output) control structure that regulates the gas sparging for membrane scouring and the frequency of physical cleaning (ventilation and back flushing). The filtration process is monitored by measuring the fouling rate on-line. This controller demonstrated its ability to keep fouling rates low (close to 0 mbar mm(-1)) by applying sustainable gas sparging intensities (approx. 0.23 Nm(3) h(-1) m(-2)). It also reduced the downtimes needed for ventilation and back-flushing (less than 2% of operating time). (C) 2012 Elsevier B.V. All rights reserved.