In this study, two methods of chemical oxidation process (COP) and natural oxidation process (NOP) were adopted to start the manganese oxide (MnOx) filter columns for removing ammonia (NH4+-N) and manganese (Mn2+) from groundwater. Transition metal element Ni was added to accelerate the start-up of filter columns NH4+-N and Mn2+ removal. The results showed that Ni-undoped COP (UCOP), Ni-doped COP (Ni-COP), Niundoped NOP (UNOP), and Ni-doped NOP (Ni-NOP) took 12 days, 5 days, 21 days, and 20 days to remove NH4+-N from 1 to 1.5 mg/L to less 0.5 mg/L, respectively, and 24 days, 20 days, 36 days, and 25 days to remove Mn2+ from 1 mg/L to less 0.1 mg/L, respectively. Ni doping accelerated the start-up of the MnOx filter columns, however, it did not significantly improve the start-up speed of NOP removal of NH4+-N. Combined with the results of characterization analysis, it was found that MnOx prepared by the two methods were different. However, the doping of Ni element caused the types of MnOx tend to be consistent, but the crystallinity of MnOx generated by COP was significantly stronger than that of NOP. In addition, Ni doping promoted the formation of oxygen vacancies in MnOx, and thus improved its catalytic oxidation activity. This study provides a new idea for the removal of NH4+-N and Mn2+ in groundwater.