Although the effects of reductive soil disinfestation (RSD) in soil sterilization have been proven in several countries, the potential risks of trace metal elements (TMEs) caused by RSD require further assessment. Here, freshly Cd-spiked soil and historically contaminated greenhouse soil were exposed to RSD and the fates of TMEs, Cd, Co, Cu, Ni, Pb, and Zn, were investigated. All RSD treatments lasted for 21 days and subsamples were collected at different time intervals. Samples were open-air incubated for another 7 days until day 28 to simulate the situation after drainage. The bioavailability and geochemical fractionation of TMEs were investigated based on single and sequential extraction procedures and the environmental risks were assessed. The results showed that RSD increased the relative abundance of Firmicutes and Bacteroidetes, and the content of functional groups, including Fe, Mn, and S compounds respirations increased after RSD, highlighting the possible reductive dissolution of FeMn oxides and precipitation of TMEs. The dissolution decreased the reducible fractions of TMEs and increased the acid-soluble fractions of Co, Ni, Pb, and Zn, in the European Community Bureau of Reference results, reflecting the activation of TMEs in soils. However, the precipitation of sulfate resulted in the stabilization of Cd and Cu in two types of soils, increased their residual fractions, and decreased their acid-soluble fractions and bioavailabilities. After drainage, because the influence caused by precipitation rapidly disappeared and the impact of FeMn oxides dissolution remained, the acid-solubility of TMEs was greater than their initial status in the two soils. Furthermore, as a highly toxic metal, the activation of Cd at 28 days caused the rapid increase of ecological risks, which is particularly concerning. The results suggest that RSD temporarily increases the potential risks of TMEs and that certain measures must be taken.