Structure, morphology and electrical behaviors of poly(3,4-ethylenedioxythiophene):poly(4-styrenesulfonate) or PEDOT:PSS thin films are investigated in the presence of protein-mediated green chemically synthesized positively charged gold and silver nanoparticles. The pure and PEDOT:PSS nanocomposite thin films are prepared by spin coating method. The presence of both nanoparticle and polymer is confirmed from X-ray diffraction, whereas composite formation is confirmed from Raman and FTIR spectroscopy. Atomic force microscopy (AFM) images show the surface morphologies of both pure and composite films, whereas average film thicknesses are obtained from AFM and X-ray reflectivity analysis. The presence of electrostatic interaction between the positively charged metallic nanoparticles and negatively charged PSS chains leads to the electrostatic shielding between cationic PEDOT and anionic PSS, which favors better charge transfer through PEDOT-PEDOT conducting paths. The increase in electrical conductivity is visualized from the current-voltage (I-V) curves, which show that the conductivity is relatively higher in the presence of silver than gold nanoparticles in the composite thin films. The conductivity of nanocomposite films is approximately five to six times enhanced in comparison with the pristine PEDOT:PSS thin films.