In this study, compartment-wise investigation of an anammox baffled reactor (AnBR) was performed. The AnBR achieved steady-state conditions after a start-up period of ∼50 days and achieved NH4 and NO2 conversion percentages of 88.5 and 99.3%, respectively. Examination of the nitrogen mass balance revealed that an AnBR with a two-compartment configuration was sufficient for nitrogen loading rates (NLRs) ranging from 0.125 to 1.975 kg N/m3/d and resulted in a nitrogen removal efficiency (NRE) of 86.7–93.7%. Higher NLRs (4.04–5.05 kg N/m3/d) required four compartments to achieve an NRE of 82.2–87.1%. Further, an overall NLR increase of up to 5.93 ± 0.23 kg N/m3/d resulted in complete AnBR failure. The maximum nitrogen removal rate was consistently recorded in the 1st compartment for all NLRs examined; as a result, this compartment exhibited the highest bacterial activity. Biomass concentration, specific anammox activity, extracellular polymeric substances, and average granule diameter in the 1st compartment with an overall NLR of 0.05 kg N/m3/d were estimated to be 11.2 gVSS/L, 0.03 mg N/gVSS/h, 84.3 mg/gVSS, and 0.65 mm, respectively. These values increased to 26.1 gVSS/L, 11.80 mg N/gVSS/h, 242.1 mg/gVSS, and 2.31 mm, respectively, when the overall NLR was incremented to 4.04 kg N/m3/d. However, a gradual reduction in bacterial activity was observed from the 1st to the 5th compartment. The microbial community analysis indicated that the dominant phyla in the 1st compartment (NLR of 0.252 kg N/m3/d) with the highest nitrogen removal were Chloroflexi (38.13%), Planctomycetes (22.62%), and Proteobacteria (14.75%).