In the European Union, organic viticulture faces enormous challenges in controlling grapevine downy mildew since the ban on inorganic phosphonates or phosphonic acid in 2013. However, inorganic phosphonate is still detected in organic wines, although the responsible winegrowers often pledge that they had not sprayed phosphonate-containing products in their vineyards. Among several hypotheses on the origin, the emergence of phosphonate from the soil, e.g., due to preceding applications or from contaminated groundwater, is in discussion. This study investigates whether an analytical differentiation of the origin of phosphonate in the plant or the final product might be feasible by examining leaf and petiole tissue. A total of 908 leaf and petiole samples of various grapevine cultivars were collected from a container vine experiment as well as from four experimental vineyard sites in Germany, on which phosphonate was either sprayed onto the plants as part of crop protection (all experiments), applied to the soil (container experiment only) or present as residue from previous applications (vineyard experiments). Phosphonate concentrations in leaves and petioles depended strongly on whether plants had been sprayed or had taken up phosphonate from the soil. Therefore, an index was created and tested using independent datasets from different geographical locations, based on the concentrations found in leaves and petioles. Index accuracy was at 99.1% correct classifications when distinguishing phosphonate origin from the soil versus that from foliar spraying. Furthermore, phosphonate uptake from the soil was shown to allow considerable phosphonate concentrations in the berries and musts, rendering associations of phosphonate residues in wines with accusations of an actual foliar application highly questionable. In brief, our data and index might provide an approach for identifying the source of phosphonate contamination in the grapevine plant and, if suitable sample material is available, also the related products.