Nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) can oxidize ferrous iron (Fe(II)) to ferric iron (Fe(III)) with nitrate as the electron acceptor under anoxic conditions. Such bacteria play important roles in soil fertility regulation, pollutant migration, and greenhouse gas emissions in ecological environmental processes. In natural environments, Fe(II) concentrations vary significantly among different ecosystems. However, most previous studies adopted a fixed Fe(II) concentration for microbial culture experiments, and the effects of Fe(II) concentration changes on the metabolic processes of the bacteria themselves remained largely unexplored. To fill this knowledge gap, a Pseudomonas NRFeOx bacterium isolated from river sediments was taken as the research object, and the effects of Fe(II) concentration on its metabolic processes were systematically evaluated, including Fe(II) oxidation, nitrate reduction, acetate oxidation, and nitrite accumulation by combining methods such as microbial anaerobic culture experiments, ion chromatography, and whole-genome sequencing analysis. The results showed that Fe(II) concentration had a relatively minor effect on the rate and extent of nitrate respiration of the strain. In contrast, Fe(II) concentration exerted a significant effect on the initiation time of its metabolic reactions. In the presence of 1 mmol/L Fe(II), nitrate reduction, Fe(II) oxidation, and acetate oxidation all started on the first day after inoculation; while in the presence of 3 mmol·L⁻¹ and 5 mmol/L Fe(II), the initiation of the above reactions was delayed to the 2nd and 6th days, respectively. Nevertheless, once the reactions were initiated, the rates and extents of nitrate reduction, acetate oxidation, and Fe(II) oxidation tended to be consistent under different Fe(II) concentration conditions. These findings indicate that changes in Fe(II) concentration are involved in the induction of certain metabolic pathways in nitrate-reducing Fe(II)-oxidizing bacteria, suggesting that Fe(II) concentration can act as a potential chemical factor to regulate the distribution and metabolic processes of different nitrate-reducing Fe(II)-oxidizing bacteria in natural environments.