This work presents the design and practical implementation of a control strategy for the operation of a sequencing batch reactor with a submerged membrane. The bioreactor is used for treating wastewater that is inhibitory for sufficiently high concentrations. The strategy combines the use of a robust feeding strategy to ensure biodegradation near an optimal unknown concentration value, using only the dissolved oxygen concentration as feedback signal, and a strategy to minimize membrane fouling based on flux and transmembrane pressure measurements during filtration. The strategy was tested on a 10 L laboratory bioreactor treating synthetic wastewater containing 4-chlorophenol as inhibitory model compound and sole source of carbon. Experimental results show the applicability of the proposed strategy.