Komagataella phaffii is an efficient system for secreted recombinant protein expression. However, this host also expresses native proteases whose activity can degrade the target proteins, thus impacting native yield and quality. This proteolysis creates impurities considered critical quality attributes (CQAs) by regulatory agencies. Capillary electrophoresis sodium dodecyl sulfate (CE-SDS) is an ideal analytical method for characterizing these impurities due to its high resolution, sensitivity, and ability to separate protein fragments, making it valuable for the control strategy and characterization of a biopharmaceutical product.