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Abstract Nitrification is the rate limiting step in the nitrogen removal processes since nitrifiers have high oxygen demand, but poorly compete with aerobic heterotrophs. In a laboratory-scaled system, we investigated a process of ammonium oxidation under ferric-iron reducing condition (feammox) in the presence of organic carbon using influents with high NH4 + and COD contents, and ferrihydrite as the only electron acceptor. Batch incubations testing influents with different NH4 + and COD concentrations revealed that the [COD]/[NH4 +] ratio of 1.4 and the influent redox potential ranging from − 20 to + 20 mV led to the highest removal efficiencies, i.e. 98.3% for NH4 + and 58.8% for COD. N2 was detected as the only product of NH4 + conversion, whereas NO2 − and NO3 − were not detected. While operating continuously with influent having a [COD]/[NH4 +] ratio of 1.4, the system efficiently removed NH4 + (> 91%) and COD (> 54%) within 6 day retention time. Fluorescence in situ hybridization analyses using Cy3-labeled 16S rRNA oligonucleotide probes revealed that gamma-proteobacteria dominated in the microbial community attaching to the matrix bed of the system. The iron-reduction dependent NH4 + and COD co-removal with a thorough conversion of NH4 + to N2 demonstrated in this study would be a novel approach for nitrogen treatment.