In this study, dark chocolates (DCh) containing zinc lactate (ZnL) were enriched with extracts from elderberries (EFrE), elderflowers (EFlE), and chokeberries (ChFrE) to improve their functional properties. Both dried plant extracts and chocolates were analyzed for antioxidant capacity (AC) using four different analytical methods: 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), cupric ion-reducing antioxidant capacity (CUPRAC), and ferric-reducing antioxidant power (FRAP), while total phenolic content (TPC) was determined by Folin–Ciocalteu (F–C) assay. An increase in antioxidant properties of fortified chocolates was found, and the bioaccessibility of their antioxidants was evaluated. The highest AC and TPC were found in ChFrE and chocolate with chokeberries (DCh + ChFrE) before and after simulated in vitro digestion. Bioaccessibility studies indicated that during the simulated digestion the AC of all chocolates reduced significantly, whereas insignificant differences in TPC results were observed between chemical and physiological extracts. Moreover, the influence of plant extracts on physicochemical parameters such as moisture content (MC), fat content (FC), and viscosity of chocolates was estimated. Furthermore, scanning electron microscopy with dispersive energy spectroscopy (SEM-EDS) was used to analyze surface properties and differences in the chemical composition of chocolates without and with additives.