Recently, 1H NMR (nuclear magnetic resonance) spectroscopy was presented as a viable option for the quality assurance of foods and beverages, such as wine products. Here, a complex chemometric analysis of red and white wine samples was carried out based on their 1H NMR spectra. Extreme gradient boosting (XGBoost) machine learning algorithm was applied for the wine variety classification with an iterative double cross-validation loop, developed during the present work. In the case of red wines, Cabernet Franc, Merlot and Blue Frankish samples were successfully classified. Three very common white wine varieties were selected and classified: Chardonnay, Sauvignon Blanc and Riesling. The models were robust and were validated against overfitting with iterative randomization tests. Moreover, four novel partial least-squares (PLS) regression models were constructed to predict the major quantitative parameters of the wines: density, total alcohol, total sugar and total SO2 concentrations. All the models performed successfully, with R2 values above 0.80 in almost every case, providing additional information about the wine samples for the quality control of the products. 1H NMR spectra combined with chemometric modeling can be a good and reliable candidate for the replacement of the time-consuming traditional standards, not just in wine analysis, but also in other aspects of food science.