BACKGROUNDPhycocyanin (PC), a natural blue photosynthetic pigment found in cyanobacteria, rhodophyta and cryptophyta has numerous applications in biotechnology and the food industry. The phycocyanin extraction method has a significant impact on its bioactivities, purity index, cost and potential applications; thus, the development of an efficient extraction strategy continues to be a primary research goal.RESULTSThis study evaluated the efficacy of different methods for the extraction of cyanobacterial phycocyanin (C‐PC) from three marine cyanobacterial isolates, namely Arthrospira platensis, Phormidium sp. and Pseudoscillatoria sp. wet biomass. The pretreatment step of soaking biomass in extraction buffer for 60 min, followed by a combination of freeze–thaw (one cycle; 2 h) and sonication (2 min) treatment was found to be the most effective extraction strategy, producing the highest C‐PC yield (16.19 ± 0.34%, 15.89 ± 0.61% and 15.56 ± 0.69% dry cell weight for strains A. platensis, Phormidium sp. and Pseudoscillatoria sp., respectively). Furthermore, a biomass‐to‐solvent ratio of 0.02 g mL−1 was optimal to attain food‐grade purity ((A620/A280) ≥ 0.7). Bioactivity evaluation of crude and purified C‐PC exhibited its potential as antioxidant compounds and as an antimicrobial agent with significant inhibitory effects against various pathogenic microorganisms.CONCLUSIONThe study proposed an efficient and cost‐effective C‐PC extraction process for cyanobacteria and highlighted the potential of C‐PC as a valuable bioactive compound with various applications. © 2024 Society of Chemical Industry (SCI).