Orthopedic implants are essential for treating severe fractures and incomplete bone regeneration. However, metal-based implants often suffer from corrosion and biocompatibility issues. This study developed 3D-printed Polylactic Acid Plus (PLA+) bone screws coated with molybdenum and zirconia (ZrO2) nanocomposites using the dip-coating method. The Taguchi method optimized five coating parameters: molybdenum weight, zirconia weight, ethanol volume, incubation time, and coating duration. The Taguchi method and Response Surface Methodology (RSM) were used for data analysis, while NSGA-II and TOPSIS determined the optimal parameters. Molybdenum weight significantly increased compressive strength (35.45%), while coating time had the greatest effect on density (25.88%). Optimization improved compressive strength/Ec (Modulus of elasticity) to 315.808 MPa and density to 1.141 g/cm3. Compressive strength was significantly improved through optimized coating parameters; however, the achieved value of 315.808 MPa requires validation due to its relatively high magnitude compared to typical PLA materials reported in the literature. The study concludes that combining the Taguchi and NSGA-II methods effectively enhances the mechanical performance and biocompatibility of biodegradable bone screws. The optimal dip-coating parameters were 0.101 g molybdenum, 0.100 g zirconia, 59.523 mL ethanol, 6.025 h of incubation, and 7.907 min of coating time. However, the study is limited to in vitro mechanical testing, and further in vivo evaluations are necessary to confirm long-term biocompatibility and performance.