A new control algorithm for performing filtration in a membrane sequencing batch reactor (MSBR) to prevent fouling is presented. Based on continuous measurements of the transmembrane pressure (TMP) and the permeate flux, the algorithm decides when to initiate backwashing. The algorithm was tested on a laboratory scale bioreactor treating synthetic wastewater containing 4-chlorophenol (4CP) as model toxic compound and filtration was carried out using a submerged tubular membrane module and a diaphragm pump. Several controller configurations were tested for different MSBR cycles. The results showed that the proposed algorithm was robust against the highly varying mixed liquor characteristics and was able to keep the TMP below critical values and maintain the flux at a maximum for most of the filtration time. Therefore, despite possible frequent backwashes, the total filtration time was minimized.