Currently, there are increasing efforts to utilize nanoremediation as an environmental technology for cleaning up polluted environments using nanoscale zero-valent iron (nZVI); however, concerns exist regarding the long-term environmental impact of this strategy. In this study, an innovative methodology for evaluating nZVI impact on soil bacteria is utilized, based on transcriptional analysis of three novel biomakers: tnaA, sodB and trx genes. At the same time, classical toxicological bioassays with the nematode Caenorhabditis elegans were performed. Microcosms treated with 1, 5 and 10 % w/w of nZVI were set up using a commercial standard soil and incubated for 21 days. The tnaA gene, involved in indole production, was significantly upregulated at all assessed nZVI concentrations, suggesting that bacterial cells used this molecule to inform the rest of the community about the changes produced upon nZVI soil treatment. The higher the exposure time, the lower nZVI concentration needed to detect these changes. Consequently, soil bacteria activate a cellular adaptive response to cope with the nZVIinduced oxidative stress, increasing the expression of genes encoding key reactive oxygen species (ROS)-scavenging enzymes; in fact, an upregulation of the sodB and katB genes was recorded upon nZVI exposure. On the contrary, C. elegans survival and growth endpoints were not affected at any nZVI concentration whereas the exposure time significantly increased nematode growth in the soil. Therefore, despite the lack of toxicity revealed by the classical conducted tests, the transcriptional analyses demonstrated the usefulness of combining the set of proposed biomarkers for early detection and monitoring the impact of nZVI on soil bacteria after environmentally important periods of exposure.