<p>Potato crop production significantly contributes to human nutritional needs. The continuous cropping of potatoes depletes the soil of macronutrients, such as nitrogen (N). Excessive use of nitrogenous fertilizers to ensure N availability has been linked to environmental pollution and greenhouse gas emissions. Thus, understanding metabolism of the potato plant, its response to N limitation and how to achieve maximum yield in poor soils, could thus be an important highway for smart crop production. Here, we present a gas chromatography—mass spectrometry -based metabolomics analysis of potato plants grown under contrasting N conditions. Data show that a reduction in N availability causes a decreased in the abundance of several amino acids but an increase in most carbohydrates. In a previous article, we have shown that the heterologous expression of a Globin/Nitric Oxide Synthase chimera (SyNOS) from cyanobacteria improves N-deficiency tolerance in Arabidopsis. This work aims to describe the effect of SyNOS expression on the N metabolism of a crop plant. Thus, we expressed SyNOS in potato, grew the resultant transgenics under contrasting N conditions, and evaluated their responses. SyNOS expression partially prevents the adverse effects of N deficiency on the contents of specific amino acids in potato. Nitrate reductase activity and mRNA levels of nitrite reductase and glutamine synthetase were less affected by N deficiency in SyNOS transgenic potato. Collectively, the results presented here indicate that sustaining an active N metabolism and recycling N-containing molecules such as arginine, nitric oxide and nitrate, are potential targets for improving potato crop production.</p>