Fermentation is an important tool in producing functional beverages through agro-industrial wastes, and medicinal and aromatic plants due to the specific content of bioactive molecules. Therefore, this study evaluated the contribution of Matricaria recutita (chamomile), Cymbopogon citratus (lemongrass), or Mentha piperita (peppermint) extracts to the phytochemical profile and potential biological effects of a functional fermented orange beverage in vitro and in silico. The concentrations of aromatic herbal extracts that yielded the best sensory performance for fermented beverages were selected for analyses that involved characterizing the fermented beverages. The beverages that received the extracts (2%) had the highest phenolic and flavonoid content and antioxidant potential compared to the control. Hesperidin (124–130 mg L⁻¹), narirutin (66–70 mg L⁻¹), chlorogenic (11–16 mg L⁻¹), caffeic (5.3–5.5 mg L⁻¹), and ferulic (1–1.7 mg L⁻¹) acids were found in the different formulations. The in silico analysis suggested that the evaluated compounds do not present a toxicity risk (mutagenicity, carcinogenicity, hepatotoxicity, and ability to penetrate the blood–brain barrier). Additionally, they can contribute to the biological effects of therapeutic importance, such as antioxidant, gastroprotective, and anti-ulcerative properties, and the Mentha piperita L. extract presented the greatest potential among the evaluated herbs for use in functional fermented beverages.