As demand for regional and organically produced foodstuff has increased in Europe, the need has arisen to verify the products’ origin and production method. For food authenticity tracking (production method and origin), we examined 286 samples of wheat (Triticum aestivum), potatoes (Solanum tuberosum), and apples (Malus domestica) from different regions in Germany for their stable isotope compositions of oxygen, hydrogen, carbon, nitrogen and sulphur. Single-variate authentication methods were used. Suitable isotope tracers to determine wheat's regional origin were δ 18O and δ 34S. δ 13C helped to distinguish between organic and conventional wheat samples. For the separation of the production regions of potatoes, several isotope tracers were suitable (e.g. δ 18O, δ 2H, δ 15N, δ 13C and δ 34S isotopes in potato protein), but only protein δ 15N was suitable to differentiate between organic and conventional potato samples. For the apple samples, 2H and 18O isotopes helped to identify production regions, but no significant statistical differences could be found between organically and conventionally farmed apples. For food authenticity tracking, our study showed the need to take the various isotopes into account. There is an urgent need for a broad reference database if isotope measurements are to become a main tool for determining product's origin.