Processing of shrimp shells for the production of chitin makes commercial use of shell waste with economic benefits. Although chitin possesses the valuable properties of a biopolymer, with many useful applications, significant environmental pollution during its production hampers growth opportunities for industrial processing. In this study, a filtration process at different molecular weight cut-offs is assessed for protein recovery from the discharged alkaline processing stream of an industrial chitin manufacturing unit. Three tubular ceramic membranes (0.1 μm, 450 D and <300 D) have been investigated under a constant temperature of 70 °C, at chosen trans-membrane pressures of 1.3–5 bar, high cross flow velocities of 3.3–3.5 m/s, and at a volumetric concentration factor of 5. Results of concentration runs indicate a significant increase of recovered proteins, between 7 and 16%, can be achieved in the concentrate stream by reducing the chosen membrane cut-offs. A second product the permeate stream – solid-free hydroxide sodium solution – can be re-utilized in the chitin production line. Retention of the organic load led to a 56% decrease of chemical oxygen demand and total bound nitrogen in the permeate stream.