The research reported here investigated microfiltration as an alternative to density-based processes for separating amaranth starch-milk produced by the pilot-scale Al-Hakkak process into a starch-rich concentrate and an aqueous stream containing the soluble proteins and carbohydrates. A Millipore ProFlux M12 Tangential Filtration System, fitted with a 1000 kDa regenerated cellulose membrane, was used as the experimental apparatus. The selected membrane retained all the starch granules, but also retained more protein than desired (protein retention was 67% and the starch-rich concentrate had a dry-basis protein content of 12%). Analysis of the feed liquor, and diafiltered concentrate, revealed the presence of some non-starch insoluble material. This material, which may have been protein-based, was present in the starch-milk produced using the pilot-scale method but not the laboratory-scale method, and its presence determined the final protein content of the diafiltered concentrate. The optimal transmembrane pressure was approximately 100–150 kPa, above which flux increased non-linearly with pressure. However, the flux–pressure relationship was weak, suggesting that higher operating pressures may be sustainable.