The present invention relates to a mainstream deammonification process for removing ammonium from wastewater that suppresses NOB growth and produces a sludge having good settling characteristics, the process comprising: clarifying the wastewater stream in a primary clarifier (12) and producing a primary effluent; directing a first portion of the primary effluent to a biological treatment reactor (14) and removing carbon to produce treated wastewater; directing treated wastewater into an integrated fixed film activated sludge (IFAS) deammonification reactor (16) integrating nitritation and anammox processes and that is provided with intermittent aeration; directing a second portion of the primary effluent to the IFAS deammonification reactor (16) by-passing the biological treatment reactor (14), and injecting this second portion only during periods of air off and refraining from injecting during periods of air on, directing the IFAS deammonification reactor (16) effluent to a secondary clarifier (18) and producing a secondary effluent and a clarifier underflow, and recycling at least a portion of the underflow to the IFAS deammonification reactor (16).