Microchip electrophoresis (ME) with electrochemical detection has been demonstrated to be a powerful tool in food analysis. However, the coupling of ME with electrochemical detection and nanotechnologies is still in its infancy, knowing that nanomaterials can significantly improve the ME analytical performance. This work reports the coupling between ME and copper nanowires (CuNWs) for the selective analysis of monosaccharides in honey samples. Also, in terms of real applicability, the study of analytical reliability of ME is an issue of paramount importance. To this end, a representative group of nine honey samples were analyzed and the results were compared with those previously obtained by HPLC-refractive index. ME-CuNWs approach allowed the separation of glucose and fructose in <250 s under optimized separation (20 mM NaOH + 10 mM H3BO3, pH 12; separation voltage + 1000 V) and detection (E = +0.70 V in 20 mM NaOH + 10 mM H3BO3, pH 12) conditions. An excellent stability of EOF during sample analysis was achieved with RSDs for migration times <2% and for amperometric currents <9%. The quantitative contents for individual glucose and fructose obtained using ME-CuNWs in comparison with those obtained by HPLC-refractive index were highly in agreement with errors <10% indicating the reliability of the approach. The excellent analytical performance obtained confirms the analytical potency of ME-CuNWs approach, enhancing the maturity of the microchip technology and opening new avenues for future implementation of applications in the field of food analysis.