Soil microbes are critical in regulating the growth and function of eucalyptus plantations. The mechanisms underlying soil microbial communities’ response to different eucalyptus plantation management practices remain elusive. In this study, we compiled datasets containing 2744 observations across global eucalyptus-planted regions and analyzed the effects of five management practices (i.e., burning, residual removal, fertilization, mixed planting, and controlling planting years) on soil microbial biomass, diversity, and structures. Our results showed that fungal community alpha diversity responds more sensitively to management practices than bacterial community alpha diversity on eucalyptus plantations. Although the implementation of management practices significantly increased the content of most soil nutrients and microbial biomass elements (excluding burning), these practices did not necessarily improve soil microbial biomass and diversity, particularly among fungal communities. Burning, fertilization, and mixing eucalyptus with nitrogen-fixing species significantly decreased the diversity of fungal communities, which were mainly impacted by soil organic carbon and total potassium content. Compared to the four other management practices, mixing eucalyptus with nitrogen-fixing species favored the growth of bacterial communities and the storage of microbial biomass nitrogen, making it the most effective management practice. However, attention should also be paid to the protection of fungal communities. In addition, these management practices significantly changed microbial community structures, which were positively correlated with the microbial biomass elements carbon and nitrogen and, to a lesser extent, soil microbial alpha diversity. Our results highlight the importance of prioritizing mixing eucalyptus with nitrogen-fixing species as a management practice and safeguarding fungal community diversity during its implementation and suggest that microbial diversity development associated with soil organic carbon and potassium contents should be given priority in eucalyptus plantation management.