Context: Spirulina (Arthrospira) exerts a wide spectrum of pharmacological activities that are largely attributed to its phycobiliprotein content, mainly to C-phycocyanin. The extraction, isolation and purification of C-phycocyanin have been studied for many years, resulting in diverse methodologies with a range of yields and grades of purity. Objective: We performed a systematic review of the literature, consulting all the available years in TOXNET, PubMed/MEDLINE and Science Direct-Scopus. Search criteria included the separation, isolation, and purification methods for C-phycocyanin from different microorganisms. Search words were: extraction, separation, isolation and purification of C-phycocyanin. Results: The combination of aqueous two-phase systems for extraction and ultrafiltration for purification results in the best yields and highest purity of the desired nutraceuticals. It is also essential to consider the freshness and species of the primary biomass, as these factors heavily influence the concentration and viability of the phycobiliproteins and therefore affect the yield and purity. Conclusion: In order to preserve the valuable properties and health benefits of nutraceuticals, such as C-phycocyanin, it is essential to seek innovative methods for isolating and purifying these bioactive substances from natural sources. The information herein gathered indicates the best methods currently available.