The present study investigates the feasibility of anoxic nitrification-denitrification in the presence of nanoscale oxides of manganese (NSOM). A template-assisted co-precipitation method was employed to synthesize NSOM. XRD and FESEM data reveal that the composite is amorphous in nature, and the particles are in nano regime (15–28 nm). The use of NSOM as an electron acceptor for the microbial mediated anoxic nitrification and the feasibility of re-oxidation of reduced NSOM coupled to denitrification was demonstrated by laboratory scale sequencing batch reactor (SBR). SBR operation lasted for 343 days in 9 different phases by varying the initial NH4+-N (100–500 mg l−1) and cycle time (0.5–2.0 d). Maximum removals of NH4+-N and total nitrogen were 126.2 ± 11.3 mg l−1 d−1 and 109.8 ± 10.9 mg l−1 d−1 respectively, in 0.5 d cycle time. Separate batch experiments were conducted to study the effect of time, pH, temperature, COD/NH4+-N ratio, and inhibitory concentrations of NH4+-N, NO2−-N, and S2−, on the anoxic nitrification process. The developed process is economical as it works in the absence of external supply of aeration and alkalinity, and reduces 70% of the requirement of COD compared to conventional nitrification-denitrification. © 2016 Elsevier Ltd