The main environmental problems associated with the mining activities are related to the production of large amounts of wastes; Different pathways are responsible for heavy metals dispersion, by air due to wind action, by water mediated by acid mine drainage and erosion, and the metals could be mobilized in the soil by different transport mechanisms. Different remediation alternatives have been studied and reported in literature. In situ stabilization is a cheaper method. The heavy metals stabilization enables the decrease of metal mobility, reactivity and toxicity in the soil, decreasing heavy metals availability and phytoavailability. Sulphate reducing bacteria (SRB) have been successfully utilized in groundwater bioprecipitation of heavy metals. In this study, this biological agent has been used in the immobilization of heavy metal in the subsurface of the soil due to its dissimilative metabolism. SRB produces hydrogen sulfide that reacts with soluble metals present in the media, generating as final product low soluble metal compounds (metal sulfides). The bio-stabilization was studied at pilot scale to determine the stabilization efficiency using biological agent, SRB. The metals studied were Fe, Cu, Pb and Zn in the contaminated smelter soil. Bioaugmentation and biomagnification were applied. After 4 months, the metal stabilization efficiency was determined by leaching with acid solution at different pH to stimulate the metal mobility. The remediation pilot scale system showed that copper, lead and iron were much more stable at pH 3.0, with only 3.7% and 1% of total metal eluted, and compared with the system without biological agent. In the case of zinc, the elution was similar with or without remediation. The metal stabilization using biological agent was successful in the contaminated smelter soil and these results are promising antecedents for full scale in situ remediation strategy.