Carbon redirection has become the desired option for sustainable and energy-efficient wastewater treatment due to its contribution to a circular economy. However, its impact on downstream processes such as nitrification and denitrification requires further investigation. This research characterizes the nitrogen removal performance, footprint, aeration mode, and microbial composition of a flow-through membrane aerated biofilm reactor (MABR) downstream of a chemically enhanced primary treatment (CEPT) carbon redirection unit. The batch and long-term studies demonstrated relatively higher nitrification rates than those reported using conventional primary treated wastewaters. The results indicated that reducing carbon in the liquid train positively impacted nitrification by achieving 87 ± 12% (1.4 ± 0.4 g/m².d) ammonia removal with an effluent 2.5 ± 2.8 mg/L ammonia concentration at a short hydraulic retention time (HRT) of 2.5 h. Despite the lower (1.9 ± 1) soluble COD:N, up to 75 ± 25% (0.6 ± 0.4 g/m².d) total nitrogen removal was achieved at 4 h HRT by implementing intermittent aeration. The batch tests using the developed biofilms showed nitrification (denitrification) capacity up to 11 ± 1.7 gNH₄-N/m².d (8.5 ± 0.5 gNO₃-N/m².d) and 2.7 ± 0.6 gNH₄-N/m².d (2 ± 0.3 gNO₃-N/m².d) corresponding to ammonia and nitrate concentrations ranging from 10–30 mg/L and 2–10 mg/L, respectively. Microbial analysis indicated that the nitrifiers such as Nitrosomonas and Nitrospira were the dominant species. The ammonia-oxidizing, nitrite-oxidizing, and denitrifying bacteria relative abundances were 10.3 ± 1.5%, 20.7 ± 1.7%, and 20.0 ± 2.8% under continuous aeration and 1.3 ± 0.07%, 1.8 ± 0.09%, and 40.5 ± 3.1% under intermittent aeration, supporting the observed ammonia and total nitrogen removal processes, respectively. Overall, the results demonstrated that MABR downstream of the CEPT behave differently; thus, design guides should be updated accordingly.