Manganese redox-stimulated bioremediation of nitrogen wastewater is receiving increasing attention. However, the nitrogen metabolic capacity and community evolution during manganese-mediated nitrogen transformation process under continued manganese domestication conditions are ambiguous. In this study, nitrogen- metabolizing microbial consortiums were incubated with synthesized Mn-humic acid complex (Mn-HA) for one month (M1), three months (M2) and six months (M3), respectively. During the Mn-HA incubation period, Bio-MnOx accompanying with bacterial consortiums (MnOB consortiums) with high TIN removal capacities were obtained. The TIN removal rates in M1, M2 and M3 were 0.220, 1.246 and 4.237 mg·L−1·h−1, respectively, which were 15.961, 90.006 and 1550.006 times higher than CK (Control Check group, no Mn-HA added group) (0.014 mg·L−1·h−1), respectively. Functional genes (amoA, AMX and narG) were most abundant in M3, which was associated with the highest nitrogen removal rate in M3. MnOB1 (bacterial consortium in M1), including Geobactor, Geothrix, Anaeromyxobacter and Bacillus, may be responsible for the Mnammox-NDMO (MnOx reduction coupled to ammonium oxidation – nitrate/nitrite-dependent low-valent Mn oxidation) process. MnOB3 (bacterial consortium in M2) enriched nitrifying bacteria Ellin6067, and denitrifying bacteria Denitratisoma, which dominated nitrogen transformation. MnOB6 (bacterial consortium in M3) enriched denitrifiers Denitratisoma, nitrifiers Ellin6067 and potential anammox bacteria SM1A02, Candidatus_Brocadia. Combined with the reduced abundance of Nitrospirae, a short-cut partial nitrification and denitrification (PND) or partial nitrification, denitrification and anammox (PNDA) could occurred in M2 and M3. It is suggested that community may have evolved into an energetically efficient short-cut nitrification, denitrification and anammox consortium to replace the full-range nitrification and denitrification community in M1 and CK under the continued manganese domestication conditions. Enhanced metabolic pathways of hydroxylamine oxidation and the nitric oxide reduction may confirm that PND or PNDA occurred in M2 and M3.