In recent years, due to the global market, the problem of food counterfeiting has greatly increased, especially for the certified-quality agri-food products. In order to detect food counterfeiting and quality, advanced quantitative techniques must be implemented. As part of the project PRIN 2022 PNRR “P20223P48S” entitled “Implementing advanced elemental and chemical analysis for quality, safety and traceability assessment of PGI and PDO agri-food products”, funded by European Union - Next Generation EU, we have evaluated the possibility to authenticate the origin of “Pistacchio verde di Bronte”, recognized by the European Union with the Protected Designation of Origin (PDO) label, by using the Fourier-Transform Infrared (FT-IR) spectroscopy. The chemical profile of this product was compared with the composition of samples originated from other growing areas of Sicily and world-wide. On the same sample-set, the colour of cotyledons and the content of polyphenols in their seeds were also quantified using traditional physicochemical techniques in order to corroborate and complement pistachio characterization by FT-IR analysis. It will be shown that in some cases FTIR analysis is able to discriminate pistachio samples originating from different geographical growing areas, also within Sicily, confirming a strong relationship between territory and chemical profile of vegetable crops. Based on these results, we believe that the FT-IR technique can be proposed as a fast and reliable analytical tool to assess, in a non-destructive way, the quality and authenticity of foodstuffs, supporting traditional analytical methods in the fight against counterfeiting.