A novel amperometric detection method based on the use of poly(3,4-ethylenedioxythiophene) (PEDOT) coated electrodes for the determination of organic and inorganic anions subsequent separation by capillary electrophoresis is presented. The analyte peak arises from the difference in the doping capability between the analytes and the buffer co-ion that affects the polymer oxidation kinetics and therefore the sampled current. A contactless conductivity detector was used simultaneously to directly compared both detection methods. LODs of 1.1, 2.6 and 4.1 μM and 2.1, 3.6 and 4.5 μM for acetate, propionate and butyrate were achieved with the PEDOT based detection method and the contactless conductivity detector respectively. Moreover, improved LODs for Cl- and NO3- and worsened LODs for SO42- and PO43- were obtained with the PEDOT based detection method which was found to perform better than the contactless conductivity detector for the determination of ions with a small effective radius. The PEDOT based detection method is very promising for its application in microfluidic devices and the development of new portable sensors for in situ analysis.