The elemental analysis of cherts is very important for understanding their geological history, formation and origin. In this work, chert samples collected from a mining complex located in the Gargano promontory (Apulia, Italy) have been investigated by laser-induced breakdown spectroscopy (LIBS) using a commercial handheld (h) LIBS instrument. In order to discriminate chert samples according to their mining site, the broadband LIBS spectra acquired on the specimens were subjected to multivariate data analysis. In particular, machine learning (ML) algorithms, including discriminant analysis (DA), support vector machine (SVM), and k-nearest neighbors (KNN), were applied to the data set from the averaged LIBS spectra of each sample dimensionally reduced by principal components analysis (PCA). Among the classifiers tested, the highest accuracy (72.34%) in identifying the chemical features of five different chert suites and discriminating their sources was achieved by Leave-One-Out Cross-Validation (LOO-CV) using the cosine KNN ML algorithm. The exclusion of PC1, which appeared to be mainly influenced by elements featuring large intra-class variation and engraved the clusterization, allowed to improve the accuracy of the classification reaching the value of 80.85% using the linear DA algorithm. The classification and discrimination between 2 classes (1 × 1) reached a high rate of correct predictions, which implied that this discrimination could be used as a subsequent mean to confirm if the class predicted in the previously performed multiclass classification was correct. In conclusion, the results of this study demonstrated that even chemically similar geological materials could be discriminated using LIBS analysis combined with appropriate multivariate chemometric data processing, in particular with the aim of recognizing and differentiating specific geological chert sources and identifying the origin of chert archaeological artifacts.