In this present study, microalgal phycobiliproteins were isolated and purified via potential biphasic processing technique for pharmaceutical as well as food applications. The algal pre-treatment techniques were studied to enhance the yield of microalgal phycobiliproteins from the biomass. The proposed methods were optimised to obtain the best recovery yield of phycobiliproteins that can be isolated from the biomass. The phycobiliproteins were further purified using liquid biphasic system. The results showed that microalgal phycobiliproteins of high purity and yield was achieved using sonication treatment (20% power, 50% duty cycle and 7 min of irradiation time) with the biphasic system, where the purification fold of 6.17 and recovery yield of 94.89% was achieved. This work will provide insights towards the effective downstream processing of biomolecules from microalgae.