Much effort has made to lessen the cytotoxicity and enhance the corrosion resistance of biodegradable magnesium alloys, for example, by depositing multilayered polymeric coatings containing hydroxyapatite. In this work, a hierarchical structure composed of ciprofloxacin (Cip)‐loaded on polyacrylic acid (PAA) and poly (ethyleneimine) (PEI) as biocompatible polymeric multilayers and calcium phosphate coating as the top layer is formed by the sol–gel method on the AZ91 Mg alloy with an intermediate layer formed by nitrogen plasma immersion ion implantation. The thicknesses of the multilayered coating and nitrided layer (Mg3N2) are 10 μm and 140 nm, respectively. The corrosion current density decreases by 95.6% and the corrosion potential in the polarization curve shifts to the positive direction by 23%. The passivation process which occurs at defects by deposition of corrosion products mitigates both galvanic and localized corrosion. Slight increase in the contact angle and surface free energy, enhanced corrosion resistance, and reduced cytotoxicity are observed from the multilayered structure. The better corrosion resistance enables better control of release of Cip. Biological assessment indicates that the antibacterial activity against Escherichia coli is improved by 100% after culturing for 24 hr and the cell viability and noncytotoxic behavior of the coated AZ91 are enhanced as well. The corrosion behavior and biological results suggest that the strategy of using a hierarchical structure composed of Cip‐loaded polymeric multilayers in conjunction with an intermediate plasma nitrided layer has large potential in the development of biodegradable orthopedic implants made of Mg alloys.