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Bacterial and fungal communities play critical roles in reestablishing vegetation structure, function and biodiversity in ecosystem restoration in arid and semi-arid areas. However, the long-term successional changes in bacterial and fungal communities that occur with artificial vegetation development are not fully understood. In this study, we investigated the successional changes in bacterial and fungal communities in Caragana korshinskii Kom. plantation over a period of 50 a (6, 12, 18, 40 and 50 a) and their relationships with key soil environmental factors in a typical agro-pastoral ecotone, northern China. The results showed that bacterial and fungal diversities (α- and β-diversity) were significantly affected by plantation age; moreover, the change in fungal community was more evident than that in bacterial community. Soil samples from 12 a plantation had the highest (P<0.05) bacterial and fungal α-diversity (i.e., abundance-based coverage estimator (ACE) and Chao1 index) at 0–10 cm depth compared with other samples. However, soil samples from plantation at the late recovery stage (40–50 a) had the highest α-diversity at 10–20 cm depth. Soil bacterial community was not significantly affected by plantation age at the genus level; but, soil fungal community was significantly affected at the genus level. Overall, Mortierella and Chaetomium were the dominant genera at natural recovery stage (0 a); Inocybe was the dominant genus at the early recovery stage (6–12 a); Inocybe and Mortierella were the dominant genera at the mid-recovery stage (12–40 a); And Mortierella, Cladosporium and Humicola were the dominant genera at the late recovery stage (40–50 a). Redundancy analysis (RDA) showed that β-glucosidase activity, total nitrogen and soil organic carbon were closely associated with bacterial community composition, while alkaline phosphatase, urease activity and total nitrogen were associated with fungal community composition, indicating that changes in enzyme activity and soil nutrients were the most important determinants of dominant genera. Furthermore, pathogenic microorganisms (Cladosporium and Humicola) were dominant in soils from 40–50 a plantation, which may affect plant growth, resulting in the decline of C. korshinskii plantation. Overall, the findings of this study improve the understanding of ecological patterns of bacterial and fungal communities in artificial vegetation and provide an important scientific basis for comprehensive ecological restoration management in arid and semi-arid areas.