This study aimed to discriminate red wines obtained from organic and biodynamic management by means of proton nuclear magnetic resonance (¹H-NMR) and metabonomic investigation. Red wines were produced from Sangiovese grapes over the three harvests 2010-2012 from two parcels of a vineyard, managed according to organic (ORG) or biodynamic (BIO) protocol, respectively. Every year the vinifications were performed with commercial selected yeasts (CSY) according to the organic protocol. Moreover, in 2012, CSY vinification was flanked by a spontaneous vinification (SPO) carried out by microorganisms naturally present on the grapes. To gain information about the effects of production year, vineyard management, vinification protocol and vines site in the field on the wine characteristics, proton nuclear magnetic resonance spectra were registered by means of a spectrometer operating at 600 MHz and multivariate analysis was carried out. Production year and vinification protocol were found to be the factors affecting most the characteristics of wine metabolome. Vineyard management seemed to have more limited consequences on the wine composition, with effects on some aminoacids (proline, aspartic acid and valine), alcohols and some polyphenols. The latter observation could not be considered as certain, as vines site in the field acted, in this respect, as a confounding element.