The most important factor for preventing nitrite oxidation is the maintenance of a high free ammonia (FA) concentration in the shortcut biological nitrogen removal (SBNR) process that nitrifies ammonia to nitrite, and then reduces it to nitrogen gas. Therefore, the application to the treatment of domestic wastewater that has relatively low FA concentration is difficult. To improve nitrite accumulation during the treatment of domestic wastewater, a cell-immobilization technology was adopted. Two types of prepolymers [alginic acid/polyethylene glycol (APEG) and polyethylene glycol (PEG)] were mixed with enriched ammonia oxidizers to produce cell-immobilized pellets. Whereas most of the removed ammonium was converted to nitrite in a cell-immobilized reactor, 30% of removed ammonium was oxidized to nitrate in a suspended growth reactor. Although stable nitrite accumulation could be achieved under low levels of ammonium, the production of nitrate was observed after the FA concentration decreased approximately to zero. This result shows that the maintenance of FA concentration is an inevitable requirement because the stable nitrite accumulation cannot be achieved using only immobilization technology.