High charge storage/injection capacity, stability, and biocompatibility are the essential criteria to be satisfied by a neural electrode to ensure the function and longevity of implantable microelectrodes for chronic neural stimulation. In this paper, electrochemical deposition of Poly (3, 4-Ethylenedioxythiophene) (PEDOT)/Molybdenum disulfide (MoS2) composite films on custom fabricated 32 channel gold Microelectrode array (MEA) is reported. The existence of MoS2 in the electrodeposited film is verified using standard material characterization techniques. The effect of the weight percentage of MoS2 in PEDOT is studied. The optimum conditions required for electropolymerization for attaining higher cathodic Charge Storage Capacity (CSC) and the effect of variation in electropolymerization conditions are determined using a custom made gold macro electrode of size 1 cm × 1 cm. The optimized conditions have resulted in a high cathodic CSC of ~375 mC/cm2, the low impedance of 118 Ω at 1 kHz and average charge injection capacity (CIC) of 25 mC/cm2 with an electropolymerization charge density of 58 mC/cm2 when PEDOT/MoS2 is electrodeposited onto a 32 channel gold MEA. Mechanical and cyclic stability of the electrodes coated with PEDOT/MoS2 is assessed using charge injection capability study before and after ultra-sonication and percentage of CSC retention after 1000 scanning cycles, respectively. The biocompatible nature of electrodes, verified using fibroblasts cell lines of Mouse origin (L929 Cell lines), indicates the suitability of these hybrid nanocomposites as efficient electrode coatings for neural electrode applications.