The agri-food industry faces challenges and opportunities in sourcing new raw materials for fermented products, driven by changing consumer priorities in health, sustainability, and diversity in this study evaluated hibiscus extracts prepared at 0.62, 1.25, and 2.50 g dried flowers per 1000 mL of water and examined the effect of fermentation with a Scoby (symbiotic culture of bacteria and yeast) over 60 h on physicochemical characteristics, antioxidant compounds, microbiology, color (CIELAB), proximate composition, minerals, and sensory attributes. Fermentation progress was tracked using standardized methods for pH, titratable acidity, total soluble solids, and antioxidant capacity. After fermentation, beverages were blended with maltodextrin (5 g/100 mL) and freeze-dried (−20 °C, −30 mmHg, 5 days). Treatment selection considered total polyphenols and flavonoids, antioxidant capacity, lactic acid bacteria counts, proximate and mineral composition, colorimetry, and sensory performance. The optimal treatment with formulation 0.625 g hibiscus flowers per 1000 mL with 9% panela (unrefined cane sugar)—showed 4.2 × 10³ CFU of lactic acid bacteria, 1.43 mg gallic acid equivalents (GAE)/100 mL total polyphenols, 7.29 mg quercetin equivalents/100 mL flavonoids, and 93.63 µg Trolox equivalents (TE)/100 mL antioxidant capacity. Proximate composition was 0.22% protein, 0.82% ash, and 6.05% moisture; iron reached 9.36 ppm. Finally, fermentation with a Scoby of moderate hibiscus extracts (0.625 g/L) and panela (9%) enables the production of a lyophilized matrix containing viable lactic acid bacteria, bioactive compounds, and minerals. This process optimizes polyphenol retention and antioxidant capacity, resulting in a product with acceptable sensory attributes and potential as a functional beverage.