While nanoscale zero valent iron (NZVI) is a promising alternative for in situ remediation, its potential environmental impact is a major concern. Herein, irreversible small colony variant (SCV) of Pseudomonas putida F1, obtained from the repetitive exposure to NZVI, was firstly reported. This SCV phenotype exhibited several altered characteristics including slower growth rate or longer lag phase, loss of swimming ability, and reduced biofilm formation. Regardless of reversibility, the persistence to gentamicin was used to distinguish the phenotypic variant from the normal phenotype and to further explore factors affecting this occurrence. By the third cycles of the repetitive exposure to 0.1 and 0.5 g/l of NZVI, the frequency of the phenotypic variant increased by 67-and 342-times, in comparison to those of non-exposed cells, respectively. While the repetitive exposure to 0.5 g/l of Fe(II) also resulted in the rising of the gentamicin-persistent phenotype by 65-fold by the third cycle of exposure, the repetitive exposure to either oxidized NZVI or Fe(III) did not induce the phenotypic variant. These results suggest that the emergence of this phenotype appears to associate with the NZVI-mediated oxidative stress. Together, this study suggests that the exposure to NZVI could trigger the emergence of phenotypic variants which could result in an environmental fitness trade-off.