Heavy metal contamination is a serious problem worldwide threatening soil environment and human health. In the present study, concentrations of 6 heavy metals at an electronic waste (e-waste) site in Nigeria were correlated to their mobility, showing distinct distribution pattern between surface soils and subsoils. Proteobacteria, Finnicutes, Acidobacteria and Planctomycetes dominated the indigenous soil microbial communities, and there was significant discrimination of bacterial taxonomic composition between the heavy metal contaminated and uncontaminated areas. The abundance of most bacterial taxa changed with heavy metal contamination level to different extent. The multivariate regression tree (MRT) analyses illustrated that main environmental variables influencing bacterial taxonomic composition included soil texture (31%) and organic carbon (14%), whereas microbial diversity was affected by soil pH (32%) and soil texture (14%). Our results surprisingly indicated that soil properties were more influential in determining soil bacterial composition and diversity than heavy metals even at the e-waste site which was seriously contaminated by heavy metals. The present study contributes to a deeper insight into the key environmental variables shaping the diversity and composition of soil microbes at heavy metal contaminated e-waste sites.