Aglianicone is an autochthonous variety of black berried wine grape cultivated exclusively in southern Italy, but with limited information on the molecular composition of its grapes. HRMAS NMR spectroscopy was used to identify the primary metabolome of Aglianicone grape pulp from two different vineyards and the observed metabolomic changes reflected the local terroir conditions or harvesting years. Moreover, the berries pulp metabolome was related to Apparent Electrical Conductivity (ECa) maps deriving from on-site near-surface geophysical measurements of vineyard soils obtained by an electromagnetic induction (EMI) technique. Most of primary metabolites of Aglianicone grape varied systematically as a function of the spatial variability of soil properties as well as vineyards terroir and harvesting years. Therefore, the proposed approach that couples HRMAS NMR spectroscopy with ECa maps of vineyard soils represents an innovative support for wine producers who can select the best vine/soil combination to ensure the maximum wine quality.