Fruit juices are one of the most widely consumed beverages worldwide, and their production is subject to strict regulations. Therefore, this study presents a methodology based on the use of headspace–gas chromatography–ion mobility spectrometry (HS-GC-IMS) in combination with machine-learning algorithms for the characterization juices of different raw material (orange, pineapple, or apple and grape). For this purpose, the ion mobility sum spectrum (IMSS) was used. First, an optimization of the most important conditions in generating the HS was carried out using a Box–Behnken design coupled with a response surface methodology. The following factors were studied: temperature, time, and sample volume. The optimum values were 46.3 °C, 5 min, and 750 µL, respectively. Once the conditions were optimized, 76 samples of the different types of juices were analyzed and the IMSS was combined with different machine-learning algorithms for its characterization. The exploratory analysis by hierarchical cluster analysis (HCA) and principal component analysis (PCA) revealed a clear tendency to group the samples according to the type of fruit juice and, to a lesser extent, the commercial brand. The combination of IMSS with supervised classification techniques reported an excellent result with 100% accuracy on the test set for support vector machines (SVM) and random forest (RF) models regarding the specific fruit used. Nevertheless, all the models have proven to be an effective alternative for characterizing and classifying the different types of juices.