This study aimed to investigate the phenolic composition, antioxidant potential, enzyme inhibitory activities and molecular docking-supported bioactivity of jujube and hawthorn in ethanolic extract and vinegar matrices. Antioxidant activities were evaluated using DPPH, ABTS, and CUPRAC assays, and inhibitory effects against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), urease, tyrosinase, elastase and collagenase were determined spectrophotometrically. Molecular docking analysis was performed to explore the interactions of major phenolic compounds with target enzymes. Vinegar samples generally exhibited higher phenolic contents and stronger antioxidant activity than the corresponding extracts, and this indicated that fermentation enhanced the functional properties of both fruit matrices. Jujube vinegar demonstrated the strongest antioxidant capacity with remarkably low half-maximal inhibitory concentration (IC50) values in DPPH (50.76 ± 1.02 μg/mL), ABTS (10.50 ± 0.10 μg/mL) and CUPRAC (13.33 ± 0.11 μg/mL) assays. Enzyme inhibition experiments revealed pronounced cholinesterase and tyrosinase inhibitory activities in jujube vinegars, and hawthorn vinegars showed particularly strong urease and elastase inhibition. In contrast, collagenase inhibition remained limited in most samples. Docking analysis demonstrated favourable binding affinities of quercetin, isoquercetin, chlorogenic acid, protocatechuic acid and quinic acid toward biologically relevant enzyme targets supporting the experimental findings. Results of this study suggest that fermentation-driven matrix transformations enhance phenolic bioavailability and multifunctional bioactivity in jujube and hawthorn vinegars and highlight their potential as promising functional food matrices with antioxidant, neuroprotective, anti-urease, anti-tyrosinase and anti-elastase properties.