Biological wastewater treatment by aerobic granular sludge biofilms offers the possibility to combine carbon (COD), nitrogen (N) and phosphorus (P) removal in a single reactor. Since denitrification can be affected by suboptimal dissolved oxygen concentrations (DO) and limited availability of COD, different aeration strategies and COD loads were tested to improve N- and P-removal in granular sludge systems. Aeration strategies promoting alternating nitrification and denitrification (AND) were studied to improve reactor efficiencies in comparison with more classical simultaneous nitrification-denitrification (SND) strategies. With nutrient loading rates of 1.6 gCOD L(-1) d(-1), 0.2 gN L(-1) d(-1), and 0.08 gP L(-1) d(-1), and SND aeration strategies, N-removal was limited to 62.3 ± 3.4%. Higher COD loads markedly improved N-removal showing that denitrification was limited by COD. AND strategies were more efficient than SND strategies. Alternating high and low DO phases during the aeration phase increased N-removal to 71.2 ± 5.6% with a COD loading rate of 1.6 gCOD L(-1) d(-1). Periods of low DO were presumably favorable to denitrifying P-removal saving COD necessary for heterotrophic N-removal. Intermittent aeration with anoxic periods without mixing between the aeration pulses was even more favorable to N-removal, resulting in 78.3 ± 2.9% N-removal with the lowest COD loading rate tested. P-removal was under all tested conditions between 88 and 98%, and was negatively correlated with the concentration of nitrite and nitrate in the effluent (r = -0.74, p < 0.01). With low COD loading rates, important emissions of undesired N2O gas were observed and a total of 7-9% of N left the reactor as N2O. However, N2O emissions significantly decreased with higher COD loads under AND conditions.