Short chain carboxylic acids known as volatile fatty acids (VFA) are important products of biological processes and as such, their measurement has long been of interest in animal husbandry, anaerobic digestions and other biologically mediated processes. While such measurements are widespread, a low cost and accurate sensor for online process monitoring is highly desirable, but as yet unavailable. An investigation into the suitability of Poly(3,4-ethylenedioxythiophene) (PEDOT) coated electrodes in sensing the concentrations of VFAs and their applicability as detector subsequent separation by capillary electrophoresis is presented. The electrodes were subjected to pulse amperometric operation, switching between their reduced and oxidized states to promote ion exchange between the polymer and electrolyte solutions containing the VFAs. The effects of the film thickness, properties of the analyte, the duration of the pulse and the electrolyte concentration on the current response, were studied. Linear calibration curves with high correlation coefficients (>0.998) were found within the range of concentrations 0.1-10 mM for sodium acetate, sodium propionate and sodium butyrate. Furthermore, the PEDOT electrodes were shown to be very stable and precise over at least one month and no film deterioration or loss sensitivity was in evidence. The role of the polymerization charge, the pulsation time as well as the electrophoresis detection cell configuration are discussed and guidelines to increase the analytical to background signal are given.