A Millipore ProFlux M12 Tangential Filtration System, fitted with a 1000 kDa regenerated cellulose membrane has been used to separate starch granules from starch milk produced by the Al-Hakkak process. However, membrane fouling was observed, and significant difficulties in cleaning the membrane were encountered. This paper describes the multi-step cleaning cycle that was developed to adequately clean the membrane between runs. Key cleaning steps were: a cold water rinse to remove loosely bound material, a protease wash to remove protein, a sodium hydroxide wash to “pre-treat” any remaining starch granules, an amylase wash to degrade the starch granules, and a final sodium hydroxide wash to remove residues from the previous step. It is expected that this cleaning method will be applicable to any membrane materials that have been fouled by the feed stream, or similar feed streams to that used in this research as it uses conditions suitable for regenerated cellulose, which is the least tolerable membrane material as far as chemical resistance and temperature are concerned.