Here, we report for the first time the use of the Click Chemistry both to modify the surface morphology and to obtain superhydrophobic properties. Using the Click Chemistry as a post-functionalization of poly(3,4-ethylenedioxythiophene) nanofibers bearing azido groups, we show that the nanostructures already present on the surface as well as the surface hydrophobicity are highly affected by the used alkyne. These results allow one to envisage extremely various strategies to modify nanostructured surfaces while introducing various functions, for example to produce biosensors or antibacterial surfaces.