This work characterises and distinguishes Italian and Asian goji berries, combining three analytical approaches to determine 5 light stable isotope ratios, 57 mineral elements and 14 carotenoids. The study analyses stable isotope ratios and provides full HPLC-DAD-MS characterisation of the carotenoid fraction in goji berries for the first time. The isotopic composition of Italian berries was characterised by δ13C values ranging between -28.2‰ and -25.7‰, δ15N between 2.3 and 7.3‰, δ34S between 2.6 and 7.9‰, and D/H between -112 and -49‰. Italian goji berries were shown to have a particular composition and interesting nutritional characteristics, specifically a higher total carotenoid content (355 mg/100 g dw mean content vs 198 mg/100 g dw) and higher content of some micronutrients: K, B, Cu, Mo, Se, and Zn. On the basis of δ34S, Y, U, Cu, Rb, zeaxanthin palmitate and total carotenoid content, discriminant analysis correctly classified all samples according to their geographical origin.