In order to understand the influence of nitrogen and lipid nutrition on the aromatic quality of wines for cognac distillation, we developed a transdisciplinary approach that combined statistical modeling (experimental central composite design and response surface modeling) with metabolomic analysis. Three Saccharomyces cerevisiae strains that met the requirements of cognac appellation were tested at a laboratory scale (1 L) and a statistical analysis of covariance was performed to highlight the organoleptic profile (fermentative aromas, terpenes, alcohols and aldehydes) of each strain. The results showed that nitrogen and lipid nutrients had an impact on the aromatic quality of cognac wines: high lipid concentrations favored the production of organic acids, 1-octen-3-ol and terpenes and inhibited the synthesis of esters. Beyond this trend, each yeast strain displayed its own organoleptic characteristics but had identical responses to different nutritional conditions.