Our goal is to establish a remote-plasma-based aerosol-assisted atmospheric-pressure plasma deposition (RAAPD) system for depositing protein–plasma-polymerized-ethylene coatings. The method of RAAPD is using plasma to polymerize ethylene and add protein aerosol at downstream region to coat protein–plasma-polymerized-ethylene on substrate. We investigated effects of different mixing, mesh, deposition distance, gas flow, voltage, and frequency. Results showed that downstream-mixing method reduced heat effects on protein. The optimal coating was achieved when using mesh, at a close deposition distance, with high flow rate of protein aerosol, and under high voltage. Compared with current methods, impacts of RAAPD include reducing effects of plasma generated heat, reactive species, and UV on protein, and deposition will not be limited by electrode area and substrate material.