A vortex fluidic device (VFD) is effective for downstream processing of C-phycocyanin (C-PC) from blue-green microalga Spirulina maxima using an aqueous two phase system (ATPS): polyethylene glycol (PEG) and aqueous potassium phosphate. The VFD-intensified ATPS continuous flow processing (VFD-ATPS) has spontaneous phase separation of the liquid exiting the 20 mm diameter tube inclined at 45° and rotating at 6550 rpm, for a 0.2 mL/min flow rate. This processing results in at least a 9.3-fold increase in phase demixing efficiency, 1.18-fold increase in C-PC purity, and 22% increase in yield compared to conventional ATPS methods. Multistage counter current distribution (CCD) using VFD-ATPS followed by removal of PEG and salt increased C-PC purity by 6-fold compared to the crude extract, with triple TOF mass spectrometry showing more than 95% sequence coverage for both subunits. This work establishes the utility of using VFD-intensified ATPS processing for protein purification and its potential as an effective new tool for rapid processing of biologically active and intact proteins.