Greek giant beans, also known as "Gigantes Elefantes" (elephant beans, Phaseolus vulgaris L.,) are a traditional and highly cherished culinary delight in Greek cuisine, contributing significantly to the economic prosperity of local producers. However, the issue of food fraud associated with these products poses substantial risks to both consumer safety and economic stability. In the present study, multi-elemental analysis combined with decision tree learning algorithms were investigated for their potential to determine the multi-elemental profile and discriminate the origin of beans collected from the two geographical areas. Ensuring the authenticity of agricultural products is increasingly crucial in the global food industry, particularly in the fight against food fraud, which poses significant risks to consumer safety and economic stability. To ascertain this, an extensive multi-elemental analysis (Ag, Al, As, B, Ba, Be, Ca, Cd, Co, Cr, Cs, Cu, Fe, Ga, Ge, K, Li, Mg, Mn, Mo, Na, Nb, Ni, P, Pb, Rb, Re, Se, Sr, Ta, Ti, Tl, U, V, W, Zn, and Zr) was performed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Bean samples originating from Kastoria and Prespes (products with Protected Geographical Indication (PGI) status) were studied, focusing on the determination of elemental profiles or fingerprints, which are directly related to the geographical origin of the growing area. In this study, we employed a decision tree algorithm to classify Greek "Gigantes Elefantes" beans based on their multi-elemental composition, achieving high performance metrics, including an accuracy of 92.86%, sensitivity of 87.50%, and specificity of 96.88%. These results demonstrate the model's effectiveness in accurately distinguishing beans from different geographical regions based on their elemental profiles. The trained model accomplished the discrimination of Greek "Gigantes Elefantes" beans from Kastoria and Prespes, with remarkable accuracy, based on their multi-elemental composition.