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.