Challenges to the reclamation of pyritic mine tailings arise from in-situ acid generation that severely constrains natural revegetation. While microbial communities that participate in acid generation through iron and sulfur (FeS) oxidation in acidic aquatic environments are well studied, relatively little information is available concerning the initial dynamics of in-situ soil acidification due to microbial FeS oxidation that occur in moderately acidic conditions. This research characterizes the taxonomic composition and behavior of microbial FeS oxidizing communities across a pH gradient from moderately acidic to highly acidic environmental conditions. We combine results from a 7-year compost-assisted phytostabilization field study with a controlled microcosm enrichment experiment that was conducted in an artificial soil matrix to follow the influence of pH on development of the soil microbiome. Microcosm results show that biological activity significantly increases the acidification rate in moderately acidic pH conditions in comparison to abiotic controls. Taxonomic profiles of the microbial communities in the microcosms and from the field study reveal that populations associated with both heterotrophic and lithotrophic activity (Alicyclobacillaceae, Acetobacteraceae and Xanthomonadaceae) dominate during acidification in moderately acidic conditions. These results suggest that chemoheterotrophs are an important element of the microbial community that help enable, directly and indirectly, lithotrophic FeS oxidation across moderately acidic conditions. Taken together, this research suggests that shifts of microbial populations associated with pH transitions have the potential to be used as bioindicators of the present and future status of the phytostabilization process.