Two Granular Sequencing Batch Reactors were operated to perform partial nitrification of sludge reject water at different temperatures, from 25–41°C. Every temperature was fixed for about a month in order to evaluate the nitritation rate, morphological features of aggregates and bacterial populations. The optimum temperature was found between 33 and 37°C in terms of nitritation rate. Morphological features of granules did not show significant changes with temperature in the range between 28 and 37°C; Feret diameter remained at 5.8±0.7 mm and roundness was 0.76±0.02. Lower temperatures promoted the appearance of filamentous bacteria, leading to an increase of the sludge volume index (SVI) and a consequent reduction of biomass concentration. When the temperature was increased to 39°C, more than the 80% of aggregates showed a diameter higher than 6 mm but density decreased from 28 to 19 g VSS L−1, resulting in an increase of the SVI from 33 to 80 mL g−1. The establishment of 41°C caused a rapid destabilization of the system and nitritation activity disappeared. Bacterial populations did not experience significant changes during the experimental period and Nitrosomonas was the dominant species at all the temperatures assayed.