The characteristics of fermented apple juice ‘Jiaosu’ as a traditional folk beverage were determined. Sequential alcoholic, acetic and malolactic fermentation was mediated either by intrinsic or inoculated microbiota over six months at room temperature under static conditions. The fermentation mixture was composed of fruits of Malus pumila Mill., var. Fuji (Rosaceae) and fruit of Citrus limon Burm. f., var. Eureka (Rutaceae), acacia honey of Robinia pseudoacacia L. (Fabaceae) and spring water at a weight ratio of 3:1:10. Product anti-oxidative features, antimicrobial capacities and the metabolic byproducts were determined at the end of fermentation. Our results showed an elevation of antioxidant activity, good antimicrobial ability and enrichment of bioactive compounds in the directed fermentation inoculated with Saccharomyces cerevisiae, Acetobacter pasteurianus and a mixture of Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus paracasei compared to the spontaneous fermentation. Prebiotic fermentation tended to preserve and even improve the antioxidant capacity throughout the fermentation process and generated valuable substances. Though it may reduce the amounts of some other bioactive compounds, the final product quality of directed fermentation was reliable. This study provides valuable information for understanding tradition functional beverages based on fermented fruits.