Adulteration of high-value agricultural products is a critical issue worldwide for consumers and industries. Discrimination of the geographical origin can verify food authenticity by reducing risk and detecting adulteration. Between agricultural products, beans are a very important crop cultivated worldwide that provides food rich in iron and vitamins, especially for people in third-world countries. The aim of this study is the construction of a map of the locally characteristic isotopic fingerprint of giant beans, “Fasolia Gigantes-Elefantes PGI”, a Protected Geographical Indication product cultivated in the region of Kastoria and Prespes, Western Macedonia, Greece, with the ultimate goal of the discrimination of beans from the two areas. In total, 160 samples were collected from different fields in the Prespes region and 120 samples from Kastoria during each cultivation period (2020–2021 and 2021–2022). The light element (C, N, and S) isotope ratios were measured using Isotope Ratio Mass Spectrometry (IRMS), and the results obtained were analyzed using chemometric techniques, including a one-way ANOVA and Binomial logistic regression. The mean values from the one-way ANOVA were δ15NAIR = 1.875‰, δ13CV-PDB = −25.483‰, and δ34SV-CDT = 4.779‰ for Kastoria and δ15NAIR = 1.654‰, δ13CV-PDB = −25.928‰, and δ34SV-CDT = −0.174‰ for Prespes, and showed that stable isotope ratios of C and S were statistically different for the areas studied while the Binomial logistic regression analysis that followed correctly classified more than 78% of the samples.