This study presents a new approach for high-performance detection sensors for MEMS-based capillary electrophoresis chips to substitute laser induced fluorescence (LIF) detection systems. The developed sensors easily integrate with well-known microfabrication techniques for glass-based microfluidic devices. Three-dimensional gold electrodes are structured in enveloping side channels by sputtering and patterned using a standard "lift-off" process. The variations in the capacitance between the electrodes in the side channels are measured as different samples and ions pass through the detection region of the capillary electrophoresis separation channel. Samples of beer, white wine and milk are each mixed in different buffer solutions, then successfully separated and detected using the developed device. The proposed high-performance detection sensors have microscale dimensions and provide a critical step towards the realization of the lab-on-a-chip concept.