Phycocyanin (PC), a sensitive hydrophilic protein with significant biological functions, is prone to denaturation in harsh environmental conditions. Here, we employ a microfluidic-assisted nanoprecipitation approach using poly lactic-co-glycolic acid (PLGA) as a protective coating material to shield PC from such conditions. Despite the complexity of microfluidic device preparation and the challenge of encapsulating water-like protein with high association efficiency, our study demonstrates the successful generation of nanosized PC-loaded particles using a 1-mm-width microfluidic device. Optimal device parameters, including a 90˚ intersecting angle, a 3-cm-length outlet channel, and a total flow rate of 396 µLmin−1, yielded particles approximately 200 nm in size with an association efficiency (AE) of around 80 %. Notably, DMSO proved to be an effective organic solvent for preserving PC. Interestingly, surfactants typically employed for stability and biocompatibility in microfluidic techniques, were found to be unnecessary in this system, potentially altering the secondary structure of PC, as indicated by circular dichroism (CD) spectra. Overall, this research confirms the feasibility of producing nanosized particles with monodisperse spherical morphology using a benchtop microfluidic device. Moreover, the enhanced association efficiency of hydrophilic protein in PLGA holds significant promise for encapsulating non-hydrophobic proteins.