We have successfully prepared poly (3,4-ethylenedioxythiophene) (PEDOT)/N-doped reduced graphene oxide (N-rGO) by electrodeposition, post-reduction, and doping N atoms with a microorganism (as a green reagent) to modify PEDOT and resolve the exfoliation and fragmentation problems of pristine PEDOT. This modification greatly improves the electrochemical properties of PEDOT, showing great potential for a bio-electrode coating material, which should have excellent electrochemical properties, stability and biocompatibility. The as-prepared PEDOT/N-rGO shows lower impedance, and higher capacitive performance and cyclical stability than pristine PEDOT due to the doping of N-rGO. An MTT assay demonstrates this modified PEDOT has good adhesion, cell viability and proliferation, similar to pristine PEDOT. This indicates that the modification process does not restrain the good biocompatibility of pristine PEDOT, which results from the doping of highly biocompatible N-rGO by this green method. The wrinkled structure, residual oxygen containing functional groups and dopant N atoms of N-rGO lead to the formation of a fluctuating surface and an increase in the hydrophilicity of PEDOT, which increase the specific surface area and cell adhesion in cell culture, respectively. Consequently, this modified PEDOT improves the electrochemical properties, and resolves the exfoliation and fragmentation problems of pristine PEDOT, while still retaining the high biocompatibility of pristine PEDOT, which is promising for a bio-electrode coating material.