A simple and robust protocol to maintain the structural feature of polymer-protein core-shell nanoparticles (PPCS-NPs) is developed based on the synergistic interactions between proteins and functional polymers. Using the self-assembly method, a broad range of proteins can be assembled to the selective water-insoluble polymers containing pyridine groups. The detailed analysis of the PPCS-NPs structure was conducted using FESEM and thin-sectioned TEM. The results illustrated that the protein molecules are located on the corona of the PPCS-NPs. While proteins are displacing between water and polymer to minimize the interfacial energy, the polymer offers a unique microenvironment to maintain protein structure and conformation. The proposed mechanism is based on a fine balance between hydrophobicity and hydrophilicity, as well as hydrogen bonding between proteins and polymer. The PPCS-NPs can serve as a scaffold to incorporate both glucose oxidase (GOX) and horseradish peroxidase (HRP) onto a single particle. Such a GOX-HRP bienzymatic system showed a ~20% increase in activity in comparison to the mixed free enzymes. Our method therefore provides a unique platform to preserve protein structure and conformation and can be extended to a number of biomolecules.