Tailing disposal technologies such as dry and wet disposal methods have a profound effect on the ecosystem of mining areas. However, the chemical speciation of metal(loid)s and microbial community structure in tailings under different disposal methods are still poorly understood. Here we compared the bioavailable fraction of metal(loid)s and the microbial community in vanadium-titanium (V-Ti) magnetite tailing profiles derived from dry and wet stockpiled methods. In wet tailings, the bioavailability of Cr, Cu, Mn, Ni, V, and Zn was higher than that in dry tailings as identified by BCR sequential extraction. Especially for Cu and Ni, the oxidizable fraction was the predominant fraction except the residual fraction, accounting for 37.2–59.0% and 23.2–36.6% of the total concentration in wet tailings, respectively. Based on 16 S rRNA high-throughput sequencing, totally 12 indicator bacterial taxa were detected in dry tailings against 68 in wet tailings. As the biomarkers in wet tailings, genera Sulfuricurvum, Geobacter, and Pseudomonas were expected to be applied to the transformation of metal(loid)s in the tailings. Our results emphasize the importance of dehydration treatment of tailings before stockpiling to minimize the environmental risks caused by toxic metal(loid)s, and provide insights into the engineering application of microbial technologies in V-Ti magnetite tailing area.