The elemental composition has been extensively used to characterize wine and to find correlations with environmental and winemaking factors. Although X-ray fluorescence (XRF) techniques offer many advantages, they have been rarely used for wine analysis. Here, we show the comparison of wine elemental composition results obtained by total reflection X-ray fluorescence (TXRF) and energy dispersive X-ray fluorescence (EDXRF) for elements K, Ca, Mn, Fe, Cu, Zn, Br, Rb, and Sr. The results obtained by TXRF and EDXRF have been additionally verified by inductively coupled plasma–mass spectrometry. The important analytical features of XRF techniques in wine science have been described, the preservation of volatile elements (e.g., Br) being one of their main advantages. In addition, we have shown that XRF techniques offer an optimal analytical approach for building large data sets containing highly reliable and reproducible results of elemental abundances in wines, corresponding soils, and grape juice. Such data sets are especially important for the geographic authentication of wine. This has been shown for 37 Austrian and Croatian wines collected together with respective soils from selected wine regions. The element abundances in soil reflect in a large portion in grape juice and finished wine suggesting that the contribution of the soil, that is, the plant uptake capacity expressed as ci(wine)/ci(soil) concentration factors, can be a highly discriminating factor for wine fingerprinting. This indeed has been proved in the present study in comparison to discrimination based only on wine element abundances. We have identified Fe, Zn, Br, Rb, and Sr as the best discriminator elements for the geographical authentication of wine. The study opens a new perspective in extending the application of XRF techniques as a cost-effective analytical tool for creating large databases of soil, grape juice, and wine element abundances for the evaluation of soil characteristics and other environmental parameters on wine composition.