The Fe/N ratio is an important control on nitrate-reducing Fe(II) oxidation processes that occur both in the aquatic environment and in wastewater treatment systems. The response of nitrate reduction, Fe oxidation, and mineral production to different initial Fe/N molar ratios in the presence of Paracoccus denitrificans was investigated in 132 h incubation experiments. A decrease in the nitrate reduction rate at 12 h occurred as the Fe/N ratio increased. Accumulated nitrite concentration at Fe/N ratios of 2–10 peaked at 12–84 h, and then decreased continuously to less than 0.1 mmol/L at the end of incubation. N2O emission was promoted by high Fe/N ratios. Maximum production of N2 occurred at a Fe/N ratio of 6, in parallel with the highest mole proportion of N2 resulting from the reduction of nitrate (81.2%). XRD analysis and sequential extraction demonstrated that the main Fe minerals obtained from Fe(II) oxidation were easily reducible oxides such as ferrihydrite (at Fe/N ratios of 1–2), and easily reducible oxides and reducible oxides (at Fe/N ratios of 3–10). The results suggest that Fe/N ratio potentially plays a critical role in regulating N2, N2O emissions and Fe mineral formation in nitrate-reducing Fe (II) oxidation processes.