There is an increasing trend to find novel sources of products with high antioxidant capacity and wild fruits are very good examples for these sources. In this study, fruits of Berberis vulgaris and Berberis crataegina, naturally grown in Bayburt province of Turkey, were tested for their physicochemical features, antioxidant capacities, phenolic compound profiles, and antimicrobial activities. The physicochemical analysis of the fruits revealed that the dry matter content, ash content, pH, and aw values were between 28.47% and 41.61%, 0.65% and 2.13%, 2.44 and 3.25, and 0.996 and 0.97, respectively. The total phenolic content of the fruits was determined by the Folin–Ciocalteu methodology, and for the determination of the antioxidant capacity of the fruits, DPPH, ABTS, and β-carotene bleaching methods were performed and a high level of antioxidant activity was observed. HPLC analysis was applied to identify the phenolic content of the fruits, and gallic acid and chlorogenic acid were found to be the dominant phenolic compounds in Berberis fruits. The water extracts of the Berberis fruits were tested against important foodborne pathogenic bacteria as potential antimicrobials. The extracts inhibited the growth of Bacillus cereus, Salmonella typhimurium, Yersinia enterocolitica, and Staphylococcus aureus at significant rates. This study revealed the potential antioxidant and antimicrobial characteristics of wild-type B. vulgaris and B. crataegina that can be used for different future applications.