The application of microelectrodes to measure oxygen and nitrite concentrations inside granules operated at 20 °C in a CANON (Complete Autotrophic Nitrogen-removal Over Nitrite) reactor and the application of the FISH (Fluorescent In Situ Hybridization) technique to cryosectioned slices of these granules showed the presence of two differentiated zones inside of them: an external nitrification zone and an internal anammox zone. The FISH analysis of these layers allowed the identification of Nitrosomonas spp. and Candidatus Kuenenia Stutgartiensis as the main populations carrying out aerobic and anaerobic ammonia oxidation, respectively.Concentration microprofiles measured at different oxygen concentrations in the bulk liquid (from 1.5 to 35.2 mg O2 L-1) revealed that oxygen was consumed in a surface layer of 100-350 μm width. The obtained consumption rate of the most active layers was of 80 g O2 (Lgranule)-1 d-1. Anammox activity was registered between 400 and 1000 μm depth inside the granules. The nitrogen removal capacity of the studied sequencing batch reactor containing the granular biomass was of 0.5 g N L-1 d-1. This value is similar to the mean nitrogen removal rate obtained from calculations based on in- and outflow concentrations.Information obtained in the present work allowed the establishment of a simple control strategy based on the measurements of NH4+ and NO2- in the bulk liquid and acting over the dissolved oxygen concentration in the bulk liquid and the hydraulic retention time of the reactor.