The design of new electrochemical devices integrating carbon nanotube sensors and their adaptation to commercial CE equipments are described. One of these designs was made for using commercial screen-printed electrodes, whereas the second was projected for coupling commercial glassy carbon electrodes. The electrochemical characterization of these devices revealed that their hydrodynamic behaviour is strongly influenced by the electrode modification with multi-wall carbon nanotubes that provided faster and/or more sensitive signals. The analytical applicability of these devices was illustrated for the CZE separation of chlorinated phenols and the MEKC separation of endocrine disruptors, where the use of carbon nanotube sensors has proved to be advantageous when compared with unmodified ones, with good electrocatalytic properties combined with acceptable background currents and a remarkable resistance to passivation.