Arthrospira platensis (commercially known as Spirulina) is an excellent source of phycobiliproteins, especially C-phycocyanin. Phycobiliproteins are significant bioactive compounds with useful biological applications. The extraction process plays a significant role in downstream microalga production and utilisation. The important pigments found in A. platensis include chlorophyll and carotenoids as nonpolar pigments and phycobiliproteins as polar pigments. Supercritical fluid extraction (SFE) as a green extraction technology for the high-value metabolites of microalgae has potential for trends in food and human health. The nonpolar bioactive compounds, chlorophyll and carotenoids of A. platensis, were primarily separated using supercritical carbon dioxide (SC-CO2) solvent-free fluid extraction pressure; the temperature and ethanol as cosolvent conditions were compared. The residue from the A. platensis cells was subjected to phycobiliprotein extraction. The phosphate and water extraction of A. platensis SFE residue were compared to evaluate phycobiliprotein extraction. The SFE results exhibited higher pressure (350 bar) and temperature extraction (50 °C) with ethanol-free extraction and increased nonpolar pigment. Phycobiliprotein yield was obtained from A. platensis SFE residue by ethanol-free buffer extraction as a suitable process with antioxidant properties. The C-phycocyanin was isolated and enhanced to 0.7 purity as food grade. This developed method can be used as a guideline and applied as a sustainable process for important pigment extraction from Arthrospira microalgae.