Pesticides and insecticides are the chemicals widely used in the agricultural industry, but their ecotoxicological effects on the environment are not still well understood. In this study, the remediation of chlorpyrifos (CP) and deltamethrin (DM) and their impacts on soil microbial diversity was investigated. Four different soils with various salinity (0%, 1%, 2% and 4%) were artificially contaminated by CP and DM. Then, natural attenuation of the pesticides in soil microcosms and their effects on soil microbial composition were studied by metagenomics. The pesticide natural attenuation analysis showed higher CP remediation in slightly saline soils with 1% and 2% salinity and faster removal of DM in 1% saline soil in comparison to non-saline control microcosm. The complete natural attenuation of the contaminants took around 60 days. The metagenomics analysis indicated that pesticide contamination had significant impacts on the soil flora and some dominant species in the control microcosm were completely eliminated by CP and DM. In addition, Paenibacillus (2% salinity and DM), Bacillus (4% salinity and CP), Paeniclostridium (1% salinity and DM) and Lachnospiraceae (1% salinity and CP) were the dominant genus by 77%, 50%, 41% and 39% relative abundances, respectively. At phylum level, the sequences belonged to Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were considerably enriched during natural attenuation of both DM and CP pesticides. Furthermore, Shannon and Simpson Indexes were identified more sensitive to the microbial community evenness, while, Chao1 and ACE indexes were changed by the community abundance. It was revealed that the highest negative impacts of deltamethrin and chlorpyrifos on the culturable and unculturable communities were related to the non-saline soil.