Microwave (MW) irradiation has been used to accelerate the functionalization of an azide functional poly(3,4-ethylenedioxythiophene) film by click chemistry. The absorption of MW energy by the conductive polymer has been exploited for localized activation of the reaction on the polymer surface. By use of an alkyne modified fluorescein derivative the reaction conditions have been optimized in a conventional MW oven, enabling the use of different sizes of substrates. The optimization resulted in a reduction of reaction times of approximately 20 h to only 2 min for bulk film functionalization. The method has been applied for anchoring of the chelating agent nitrilotriacetic acid (NTA) on the conductive polymer. The chelating linkage ability of NTA on the surface was investigated through a sandwich ELISA study confirming the selective bonding of a histidine tagged protein.