© 2019 Elsevier Ltd The objective of our research was to contrast the resonance techniques on tubers with the more commonly used morphological analyses. With the aims of establishing a classification among ecotypes and food fingerprint of mashua tuber, a multivariable data analysis like principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA), were performed with morphological and metabolomic profiling data. Accordingly, the morphological traits showed a clear separation among most of the studied ecotypes. For a 1H NMR metabolic profiling, at least 35 compounds were identified in tubers. The relative concentration of these compounds was used to perform a PCA and OPLS-DA analysis. A clear separation, according to PC1 = 31.7%, was between TTE_01 & TTE_02 and the ecotypes TTE_06 and TTE_05 with significantly higher concentrations of disaccharides such as maltose and sucrose. Amino acids such as proline and alanine were found and organic acid including succinic, fumaric, formic and acetic acid. In contrast, TTE_05 and TTE_06 ecotypes contained higher concentrations of monosaccharides such as fructose, glucose. Metabolic profile demonstrated to be a more reliable technique than morphological analysis for classification of ecotypes.