Phycobiliproteins (PBPs) are highly water-soluble accessory pigments derived from cyanobacteria and red algae, where they function as integral components of the light-harvesting apparatus. The major representatives of this class, namely, phycoerythrin (PE), phycocyanin (PC), and allophycocyanin (APC), are of industrial importance because of excellent coloration, strong fluorescence, and diverse biological activities. The applications extend across biotechnology, pharmaceuticals, food, and cosmetic industries, where they are valued as natural colorants, bioactive compounds, and fluorescent markers. Commercial use of PBPs requires careful validation to ensure consistency, safety, and product stability. This chapter outlines standardized laboratory protocols for evaluating PBPs, including detailed descriptions of materials, reagents, and analytical instruments required for testing. Methods for assessing purity, detecting microbial and chemical contaminants, and evaluating stability under variable pH, temperature, light, and storage conditions are provided. Collectively, these procedures serve as a practical guide for both researchers and industry professionals involved in quality control and safe use of PBPs.