A mathematical model was used to evaluate the effect of the aeration pattern and ammonium concentration in a partial nitritation-anammox sequencing batch reactor with granular and flocculent sludge. In the tested conditions, model results indicate that most of the aerobic ammonium oxidation potential would occur in the bulk liquid, with 70% of the ammonium-oxidizing bacteria (AOB) biomass in suspension rather than in granules. The simulated granular sludge consisted predominantly of anammox bacteria with AOB present in the outer layer of the granule (50m AOB layer, accounting for 3% of the granule weight). Simulation results indicated that when granules do not contain any AOB, the amount of granular biomass required to achieve the same level of nitrogen removal would strongly increase (in the simulated conditions, by a factor of three) due to anammox inhibition by oxygen. This underlines the importance of a small fraction of AOB present in the granular anammox sludge. The aeration pattern had an important impact on the nitrogen removal: a better performance was suggested for continuous aeration (90% N-removal) than for intermittent aeration (68-84% N-removal). Anammox inhibition during the periods of high oxygen concentration was identified as the main reason for the lower nitrogen removal in the intermittently aerated system. With increasing oxygen concentration, a higher residual (effluent) ammonium concentration was needed to assure nitrite-oxidizing bacteria repression in the system. This study contributes to further understand the complexity of a reactor with both granular and flocculent sludge and the impact of operation conditions on reactor performance.