The advances in therapeutics based on biological macromolecules and their pharmaceutical market have stimulated the development of separation and purification techniques like ion-exchange chromatography (IEC). In this regard, the effectiveness of biological therapies depends on high-purity protein fractions. Although, there are a few differences in each protein batch due to the amplification method or the degradation effect, which cause undesirable effects on patients. In this sense, the implementation of a reliable method like IEC is fundamental, and in recent years it has been adopted as a reference technique for protein separation and purification. Therefore, this chapter details the modification of resins to improve their sensitivity and the analysis and adjustment of variables to perform a successful protein separation by IEC.