In the present research, the applicability of stable isotope (δ13C, δ15N, δ34S, δ18O) and multi-element (P, S, Cl, K, Ca, Zn, Br, Rb, Sr) data for determining the geographical origin of garlic (Allium sativum L.) at the scale of Slovenia was examined. Slovenia is a rather small country (20273 km2) with significant geological and biological diversity. Garlic, valued for its medicinal properties, was collected from Slovenian farms with certified organic production and analyzed by elemental analyzer isotope ratio mass spectrometry combined with energy dispersive X- ray fluorescence spectrometry. Multivariate discriminant analysis (DA) revealed a distinction between four Slovenian macro-regions: the Alpine, Dinaric, Mediterranean and Pannonian. The model was validated through a leave-10%, 20% and 25% out cross validation. The overall success rate of correctly reclassified samples was 77% (on average), indicating that the model and the proposed methodology could be a promising tool for rapid, inexpensive and robust screening to control the provenance of garlic samples.