Electrochemical methods for nitrate detection are very attractive since they are suitable for in-field and decentralized monitoring. Copper electrodes are often used to this aim as this metal presents interesting electrocatalytic properties towards nitrate reduction. In this research, we study improvements in the electrochemical analysis of nitrate in natural water and food by taking advantage of the detection capabilities of ensembles of copper nanowire electrodes (CuWNEEs). These electrodes are prepared via template electrodeposition of copper within the nanopores of track-etched polycarbonate (PC) membranes. A critical step in the preparation of these sensors is the removal of the template. Here, we applied the combination of chemical etching with atmospheric plasma cleaning which proved suitable for improving the performance of the nanostructured copper electrode. Analytical results obtained with the CuWNEE sensor for nitrate analyses in river water samples compare satisfactorily with those achieved by standard chromatographic or spectroscopic methods. Experimental results concerning the application of the CuWNEEs for nitrate analysis in food samples are also presented and discussed, with focus on nitrate detection in leafy vegetables.