In this study, La Rioja wine terroir was investigated by the use of (1)H NMR metabolomics on must and wine samples. Rioja is a small wine region in central northern Spain which can geographically be divided into three subareas (Rioja Alta, Rioja Baja, and Rioja Alavesa). The winemaking process from must, through alcoholic and malolactic fermentation, was followed by NMR metabolomics and chemometrics of nine wineries in the Rioja subareas (terroirs). Application of interval extended canonical variate analysis (iECVA) showed discriminative power between wineries which are geographically very close. Isopentanol and isobutanol compounds were found to be key biomarkers for this differentiation.