In a moving bed biofilm reactor (MBBR) system, the vast majority of biomass is immobilized as biofilm besides small amounts of suspension. In this study, the influence of the individual biomass components of a deammonifying MBBR, the biofilm on carriers (BC), residual suspended biomass (SB) with a volatile suspended solids concentration of 0.09 ± 0.03 g/L, and its combination (BC + SB) on nitrogen removal efficiency was investigated. While the performance was highest for BC + SB (0.42 kg N/(m3·d)), it was reduced by a factor of 3.5 for BC solely. SB itself was only capable of nitrite accumulation. This suggests a high abundance of AOBs within suspension besides the coexistence of AOBs and anammox bacteria in the biofilm, which could be supported by results using fluorescence in situ hybridization (FISH). Thus, small amounts of suspended microorganisms can positively influence the deammonification’s efficiency. If this fraction is partially washed out, the system recovers nevertheless within hours.