Biocontrol agents play a crucial role in agricultural production by reducing the use of pesticides and chemical fertilizers, controlling pests and diseases, and enhancing crop yield and quality. While extensive research has focused on the growth-promoting and yield-increasing effects of biocontrol agents on herbaceous plants, their impact on woody crops such as trees and shrubs has not been reported. This study investigates the effects of the actinomycete strain Act12, applied via root drenching and foliar spraying, on the flowering and fruit set rates, leaf physiology and enzyme activity, and fruit characteristics and yield of the jujube tree (Ziziphus jujuba Mill.). Additionally, this study analyzes the physicochemical properties of the soil and the diversity and community structure of its microorganisms. The results indicate that treatment with Act12 significantly altered the α and β diversity of soil microorganisms and enhanced the interaction networks among them. This led to increased levels of available nitrogen, phosphorus, and potassium in the soil, significantly improving nutrient availability. Consequently, there was an improvement in the number of flower buds and fruits, as well as an increase in the longitudinal diameter and individual fruit weight of the jujube. These effects significantly enhanced the yield and total sugar content of the winter jujube. Given these findings, Act12 can be considered an effective microbial agent for enhancing the yield and quality of winter jujube when applied to the soil.