There is a growing interest among the public in fruit with a positive impact on human health. Two goji berry cultivars (‘No. 1’ and ‘New Big’) were propagated in vitro, grown in an orchard and then evaluated for macro- and microelements and harmful heavy metals (i.e., Pb, Ni, and Cd). The leaves and fruit were also assessed for nutritional value, polyphenols and the antimicrobial activity of the leaves. ‘New Big’ was characterized by a higher content of macro elements in the leaves (in vitro and orchard) and a higher content of microelements in the fruit. The harmful substances content was below the minimum value. Furthermore, neither the fruit nor the leaves contained cadmium. This study also indicated that leaves had a higher content of polyphenols compared to the fruit. The fruits were characterized by their health-promoting capacities, while the leaves were characterized by their antibacterial activity. Among the Gram-positive bacteria, the most sensitive strain was Bacillus subtilis, and among the Gram-negative bacteria, it was Proteus vulgaris. Taking into consideration the Recommended Daily Allowance (RDA) for minerals, goji berries can be declared to be a source of Cu, Fe, Mn, Zn and P.