The fabrication of biocompatible and antibacterial coatings on metallic implants remains a significant challenge for load‐bearing orthopedic implants. This study focuses on the electrophoretic deposition of chitosan/gelatin/Ag‐Mn doped mesoporous bioactive glass nanoparticles (Ag‐Mn MBGNs) composite on the PEEK/bioactive glass layer (called as multi‐structured coatings), which had been deposited electrophoretically on 316L stainless steel. The EPD parameters for the deposition of the chitosan/gelatin/Ag‐Mn MBGNs coatings were optimized via Taguchi design of experiment approach. Scanning electron microscopy images confirmed that the chitosan/gelatin/Ag‐Mn MBGNS layer was deposited on the PEEK/BG layer. The addition of biologically active metallic ions (Mn and Ag) and molecules (chitosan) showed a strong effect on the growth of bacteria. Moreover, the inclusion of Mn and Ag showed a negligible toxic effect on the bioactivity (the ability of the coating to form a bond with the natural bone) of the coatings. Furthermore, the multi‐structured coatings presented appropriate wettability and surface roughness for orthopedic applications. Overall, this study provides a direct solution to improve the bioactivity, antibacterial activity, and surface properties of deposited chitosan/gelatin coatings on orthopedic implants that are more manufacturable and translational from research to an industrial scale.