Pressure-driven membrane separations operated in the diafiltration mode appear promising as an efficient demineralization method of waste protein hydrolysates from leather production. The conclusion drawn from our experimental results is that nanofiltration membranes should be used rather then ultrafiltration ones as they show complete passage of the salts with high retention of the protein hydrolysates. In addition to the classical membrane separation operating parameters, which are crossflow fluid velocity, transmembrane pressure difference, and temperature, the required residual salt concentration as well as acceptable protein losses affect the effectiveness of the process.