The fate and behaviour of nitrogen and phosphorus were examined in semi-continuous pilot-scale aerobic digestion of waste activated sludges from an Extended Aeration, biological nutrient removal facility and a High Rate, activated sludge facility. Due to nitrification in the poorly buffered digesters, mixed liquor pH (MLpH) levels as low as pH 3.5 were observed; to counteract this, chemical MLpH control was initiated, with the goals of enhanced metabolic activity and digester efficiency. The inorganic chemicals used for this purpose (Ca(OH)2 and NaHCO3) also had substantial effects on nitrogen and phosphorus forms and concentration; digester supernatant quality was directly influenced by reactor MLpH level and controlling chemical, for both nutrients. It was concluded that chemical control of MLpH, for the enhancement of aerobic digestion, is at the same time an effective method for the removal of nuisance nutrient species, and a means of ensuring efficient overall operation of the digester.