In this paper, the synthesis of porous manganese substituted hydroxyapatite (Mn-HAp) coating on zinc oxide (ZnO) coated stainless steel (316L SS) using the electrodeposition technique is reported. The structural, functional, morphological, and elemental analyses are characterized by various analytical techniques including X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). Results of electrochemical techniques such as cyclic polarization and impedance show that the Mn-HAp coating on ZnO coated 316L SS has the highest corrosion resistance in simulated body fluid (SBF) solution. Moreover, dissolution of metal ions was extremely reduced, as evaluated by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). The adhesion and hardness of Mn-HAp/ZnO bilayer coatings have superior mechanical properties over individual coatings. Further, the biocompatibility of in vitro osteoblast attachment, cell viability, and live/dead assessment also confirmed the suitability of Mn-HAp/ZnO bilayer coating on 316L SS for orthopedic applications.