The supernatant of an anaerobic digester was treated at 20 °C in two systems. The first one is a two units configuration, conformed by two sequencing batch reactors (SBR), carrying out partial nitrification and Anammox processes, respectively. Partial nitrification was achieved by granular biomass with a mean diameter of 3 mm, operating at a dissolved oxygen concentration of 2.7 mg/L. The combined system allowed the removal of nitrogen loading rates around 0.08 g N/(L d). Afterwards, Anammox biomass was spontaneously developed in the inner core of the nitrifying granules of the SBR and therefore, partial nitrification and Anammox process were carried out in a single unit. Once the stable CANON process was established, a mean nitrogen removal rate of 0.8 g N/(L d) was registered. The settling velocities of the granules ranged from 70 to 150 m/h with sludge volumetric index values lower than 50 mL/g VSS during the whole operation.