Modification of W5O14 and MoS2 nanostructures was carried out using 3,4-ethylenedioxythiophene monomer in a capacitively coupled, RF rotating plasma reactor. Raman spectroscopy and X-ray diffraction (XRD) measurements were used for structural characterization. The surface morphologies of nanomaterials were investigated using transmission electron microscopy. Polymer coated (W5O14/PEDOT, MoS2/PEDOT) and untreated (W5O14, MoS2) nanostructures were used as the counter electrode for dye-sensitized solar cells. Photovoltaic performances of W5O14/PEDOT and MoS2/PEDOT hybrid nanostructures were higher than those of W5O14 and MoS2 inorganic nanostructures. Our results indicate that plasma polymer coated W5O14 and MoS2 nanostructures of the device for cathode increase both its fill factor and its energy conversion efficiency.