Digestate produced by cofermentation of agricultural waste and manure can be difficult to dispose of because its high ammonium content impedes its use in agriculture due to generation of odor and overfertilization. This study investigated the possibility of treating such nitrogen-rich digestate with aerobic granular sludge depending on the nitrogen load in the reactor. At nitrogen loading rate of 1.0 g TN/(L·day), the nitrogen removal efficiency was high (64.9 ± 9.8%), ammonium nitrogen was completely oxidized, and nitrate was the main nitrification product. At nitrogen loading rate of 3.4 g TN/(L·day), ammonium oxidization was still good (93.6 ± 2.0%), but the percentage of partial nitrification was high (over 68%) and nitrogen removal efficiency worsened to 30.2 ± 2.6%. Despite this, the overall amount of nitrogen removed was 0.86 g TN/(L·day) and was over nearly two times higher than at the lower nitrogen loading rate. At both nitrogen loading rates, in the effluent nitrogen in a form of suspended solids predominated. To diminish the overall N loading in the effluent, treatment is therefore recommended enabling removal of solids, e.g., microfiltration, should be applied, or the digestate should be separated into solid and liquid phases, and only the liquid fraction should be subjected to biological treatment. At high N load in aerobic granules, a very versatile community of N-metabolizing microorganisms was present. More than 50% of all bacteria in aerobic granules were able to metabolize nitrogen, and the predominant genera (35%) was Thauera, which indicated that stable ammonium removal was achieved mostly as a result of heterotrophic nitrification.