Abstract Fe(III) bio-reduction provides a prospect of applying the iron redox cycle to nitrate remediation in the aquatic environment. The objective of this study was to realize multiple nitrate removals in the system containing Shewanella oneidensis MR-1 (S. oneidensis MR-1) and ferrihydrite or magnetite. The results showed that with three periods of 30 mg·L−1 NO3−-N addition, all nitrate reduction was completed within 170 h. In the first period (0–30 h) of nitrate addition, the main contribution of nitrate removal was due to the biological reduction process by S. oneidensis MR-1, accompanied by the reduction of Fe(III). During the second (45–90 h) and third periods (100–170 h) of nitrate addition, oxidation of biogenic Fe(II) coupled with the reduction of nitrate took place. This redox reaction resulted in the production of gaseous nitrogen of 47.33% and 16.8% for ferrihydrite/S. oneidensis MR-1 and magnetite/S. oneidensis MR-1 systems, respectively. In addition, nitrite, as an intermediate product, accumulated and negatively affected nitrate removal after the third addition of nitrate. By comparing the patterns of X-ray diffraction of the iron minerals before and after the bio-reduction, it was found that ferrihydrite was transformed into magnetite, while magnetite kept its original crystal form.