Gardenia fruit, a medicinal and edible resource rich in bioactive compounds, faces several limitations, including low extraction efficiency, poor stability, and intense bitterness. In this study, gardenia fruit powder at varying concentrations (2.5%, 5.0%, 7.5%, 10.0%, and 12.5%) was mixed with a kombucha inoculum and fermented for 8 days to develop functional beverages. The results demonstrated that fermentation with gardenia fruit powder effectively supported SCOBY growth. The 5.0% addition of gardenia fruit (G5Fer) produced thicker bacterial cellulose, higher total titratable acidity (10.43 g/L), and increased total polyphenols (37.12 mg GAE/100 mL) after 8 days of fermentation. G5Fer also achieved the highest sensory scores, especially in aroma, flavor, and overall acceptance. Higher doses of gardenia fruit (≥7.5%) caused turbidity, dark color, and strong sourness, leading to lower sensory scores. Non-targeted metabolomics revealed that kombucha fermentation reshaped the metabolic profile, enriching phenolic acids (e.g., gallic acid and caffeic acid) and flavonol glycosides (e.g., kaempferol-3-O-rutinoside) via the biosynthesis of phenylpropanoid pathways while antioxidant activity (DPPH and ABTS⁺ scavenging rate) was well maintained. Overall, G5Fer achieved the best balance among acidity, bioactive compounds, and consumer preference. In conclusion, gardenia fruit represents a promising substrate for developing a functional, palatable kombucha-like beverage, aligning with the growing demand for value-added fermented products.