Nanoscale zero-valent iron (nZVI) is a promising technology for remediation of halogenated pollutants. However, the major concern is the effect of nZVI on indigenous microbial community of the polluted site. In this study, we investigated the effects of nZVI and palladized nZVI (Pd-nZVI) on remediation of halogenated organic pollutants such as decabromodiphenyl ether (DBDE) and triclosan (TCS) in soil, and simultaneous impact of nanoparticles on native microbial community of the soil system using both bare and modified nZVI. Soils collected from polluted sites were incubated in anaerobic reactors with the above nanoparticles and pollutants. Within three weeks, >80 % of DBDE was debrominated in reactor added with unmodified nZVI while the debromination was very slow with modified nZVI. TCS was completely dechlorinated within three weeks with Pd-nZVI. PCR-DGGE analysis of 16S rRNA gene analysis revealed that there were no significant changes in the diversity of bacterial community in both bare and modified nZVI added reactors. In contrast, in aqueous system unmodified nZVI showed significant shifts in the bacterial diversity. This study indicates that in soil system the toxicity of nZVI/Pd-nZVI is hindered by the heterogeneity of soil constituents. Therefore, the soil microbial diversity remains sustained during nZVI treatment.