The seeds of Phaseolus vulgaris are a rich source of protein consumed around the world and are considered as the most important source of proteins and antioxidants in the Mexican diet. This work reports on the 1H NMR metabolomics profiling of the cultivars Peruano (FPe), Pinto (FPi), Flor de mayo (FM), Negro (FN) and Flor de junio (FJ). Total phenolics, total flavonoids and total protein contents were determined to complement the nutritional facts in seeds and leaves. According to our results, the metabolomics fingerprint of beans seeds and leaves were very similar, showing the presence of 52 metabolites, 46 in seeds and 48 in leaves, including 8 sugars, 17 amino acids, 15 organic acids, 5 nucleosides and 7 miscellaneous compounds. In seeds, free amino acids were detected in higher concentrations than in the leaves, whereas organic acids were more abundant in leaves than in seeds. With multivariate and cluster analysis it was possible to rank the cultivars according to their nutritional properties according to NMR profiling, then a machine learning algorithm was used to reveal the most important differential metabolites which are the key for correct classification. The results coincide in highlighting the FN seeds and FPe leaves for the best nutritional facts. Finally, in terms of cultivars, FN and FM present the best nutritional properties, with high protein and flavonoids content, as well as, a high concentration of amino acids and nucleosides.