In neuroscience the use of a microelectrode array allows the detection of neuroelectric signals with high temporal resolution in a confined space within the tissue, while two-photon laser scanning microscopy provides high spatial resolution in a wide region of interest. The combination of these two techniques promises better understanding of the operation of neural pathways. To facilitate this connection, we studied the direct electrochemical deposition of the conductive polymer poly-2,3-ethylenedioxy-thiophene onto different Pt and Pt/Ir electrode surfaces from non-aqueous solvents, such as ionic liquid and propylene carbonate. We show the effects of electrochemical deposition technique (pulsed or continuous), monomer concentration range and solvent electrolyte type on the formation of photoluminescent - conductive films. For these variables we determined the optimal deposition parameters given as 0.025–0.050 M EDOT monomer concentration in BMIMBF4 ionic liquid and the use of pulsed deposition process to form an adherent, uniform functional electrode coating. Display omitted •Photoluminescent, conductive PEDOT layer can be deposited on neural microelectrode arrays by direct electropolymerization.•The structure of PEDOT layer can be controlled by the number, length and voltage of electric pulses applied in the process.•Optimization of applied monomer concentration is important to avoid the formation of detached polymer particles.•BMIMBF4 ionic liquid is a better electrolyte for the polymerization process than PC(LiClO4).