Color additives, also known as food colorings, are substances added to food and beverages to enhance their visual appeal and consumer acceptance. The color of a food product serves as an indicator of attributes like flavor, safety, and nutritional value. Unlike other natural colors, blue-colored fruits and vegetables are rare, making blue associated with synthetic food coloring. Phycocyanin (PC), a natural blue pigment found in Spirulina, has garnered attention for its various biological properties, including antioxidant and anti-inflammatory activities. However, its industrial application limited by susceptibility to factors like high temperatures and pH variations during processing. Encapsulation, a technique involving the trapping of bioactive ingredients in carriers, can address these issues. In this study, chitosan derivatives, Carboxymethyl Chitosan (CMC)-Whey Protein Isolate (WPI) used as a coating for complexes in the encapsulation of phycocyanin. Encapsulation employed to improve pigment stability, and the study investigates the impact of ratios, pH, and CaCl2 concentration addition as a crosslinking agent. The selection of the appropriate CMC-WPI ratio is crucial for achieving good physicochemical properties, high encapsulation efficiency, and survivability against gastrointestinal and storage conditions. The encapsulated phycocyanin demonstrates stability across various pH values, with the concentration of CaCl2 influencing particle diameter and shape.