ABSTRACT As nitrogen discharge limits are becoming more stringent, short‐cut nitrogen systems and tertiary nitrogen polishing steps are gaining popularity. For partial nitritation or nitritation–denitritation systems, anaerobic ammonia oxidation (anammox) polishing may be feasible to remove residual ammonia and nitrite from the effluent. Nitrogen polishing of mainstream nitritation–denitritation system effluent via anammox was studied at 25°C in a fully anoxic moving bed bioreactor (MBBR) (V = 0.45 m3) over 385 days. Unlike other anammox based processes, a very fast startup of anammox MBBR was demonstrated, despite nitrite limited feeding conditions (influent nitrite = 0.7 ± 0.59 mgN/L, ammonia = 6.13 ± 2.86 mgN/L, nitrate = 3.41 ± 1.92 mgN/L). The nitrogen removal performance was very stable within a wide range of nitrogen inputs. Anammox bacteria (AMX) activity up to 1 gN/m2/d was observed which is comparable to other biofilm‐based systems. It is generally believed that nitrate production limits nitrogen removal through AMX metabolism. However, in this study, anammox MBBR demonstrated ammonia, nitrite, and nitrate removal at limited chemical oxygen demand (COD) availability. AMX and heterotrophs contributed to 0.68 ± 0.17 and 0.32 ± 0.17 of TIN removal, respectively. It was speculated that nitrogen removal might be aided by denitratation which could be due to heterotrophs or the recently discovered ability for AMX to use short‐chain fatty acids to reduce nitrate to nitrite. This study demonstrates the feasibility of anammox nitrogen polishing in an MBBR is possible for nitritation–denitration systems. Biotechnol. Bioeng. 2016;113: 635–642. © 2015 Wiley Periodicals, Inc. In this pilot‐scale study adaptation and usefulness of anammox in an MBBR for nitrogen polishing is demonstrated. Almost 1‐year long study was conducted on mainstream municipal wastewater.