The fabrication and characterization of a fully integrated capillary electrophoresis (CE)-based microfluidic device with integrated carbon sensing electrode is described in this study. A combination of microfabrication protocols were employed for fabricating the hybrid polydimethyl siloxane (PDMS)/glass microfluidic device including chemical wet etching, soft lithography, and micromolding techniques. The microdevice is comprised of glass substrate with integrated gold electrodes and carbon sensing electrode, and PDMS slab that encompasses the microchannels network. The carbon sensing electrode was physically characterized via atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Raman spectrometry. In addition, its quality was evaluated electrochemically and compared to commercial glassy carbon electrodes upon performing cyclic voltammetric analysis of two illicit drugs, morphine and codeine. The analytical performance of the standalone microdevice was evaluated upon testing the injection and amperometric detection on the carbon sensing electrode using morphine and codeine as selected targets. The carbon sensing electrode provides stable background current during the application of a high sensing potential, which is necessary for sensing molecules that can be only detected at high potentials such as morphine and codeine.