The paper focused on the co-production of high-value-added product thermostable C-phycocyanin (C-PC) and biomass, further utilized in pyrolysis. The photobiosynthesis of CPC was carried out by the thermophilic cyanobacteria Synechococcus PCC6715 cultivated in the helical and flat panel photobioreactors (PBR). Despite the application of different inorganic carbon sources, both PBRs were characterized by the same growth efficiency and similar C-PC concentration in biomass. To release the intracellular C-PC the biomass was concentrated and disintegrated by the freeze-thaw method. The crude C-PC was then further purified by foam fractionation (FF), aqueous two-phase extraction (ATPE), membrane techniques (UF) and fast protein liquid chromatography (FPLC). Each of the tested methods can be used separately; however, from a practical and economic point of view, a three-stage purification system (FF, FPLC and UF) was proposed. The purity ratio of the final C-PC was about 3.9, which allows it to be classified as a reactive grade. To improve the profitability of 3G biorefinery, the solid biomass residue was used as a substrate to pyrolysis process, which leads to production of additional chemicals in the form of oils, gas (containing e.g. H ₂) and biochar.