Mining is a major threat for tropical rainforests as it induces rapid land degradation. Reforestation of mined areas is important to mitigate degradation and biodiversity losses. Microbial diversity, which serve as a good indicator of environmental perturbations, is crucial for reforestation and ecosystem functioning. Yet, limited information is available on how it is influenced by mining. We investigated the bacterial and fungal taxonomic alpha (richness and abundance) and beta diversities (Bray–Curtis dissimilarities (BCD)), root traits and nutrients among mined, undisturbed, and reforested soils in a tropical rainforest in Hainan Island (China). Soil organic matter (SOM) content was highly associated with bacterial and fungal abundances, fungal species richness, and BCD. Mining‐led vegetation removal largely reduced the SOM, and it decreased bacterial and fungal abundances, fungal species richness, and BCD. After using mined soil to plant multiple fast‐growing tree species, the root traits functioned at the levels of an original secondary forest, and it quickly recovered SOM. This process restored bacterial and fungal abundance, fungal species richness, and BCD to originally undisturbed levels. We further conclude that (i) soil fungal diversity in tropical rainforest is more sensitive to mining and reforestation than bacterial diversity. This could be attributed to largely reduced/increased SOM resulting from loss/gain in vegetation during mining/reforestation, respectively. (ii) Reduced SOM, after mining and removal of vegetation, has profound negative influences on tropical rainforest. (iii) Use of mined soil as a post‐mining substrate along with fast‐growing tree species ensures the recovery of SOM during reforestation, which alleviates the negative impacts of mining on tropical rainforests.