Three aerobic granular sludge systems were operated as sequencing batch reactors (SBR) with acetate, ethanol and glucose as carbon source. The SBR cycle was 6 h, with an anaerobic phase followed by an aerobic phase. The acetate granules (> 1.5 mm) had the greatest microbial diversity and better results in terms of removal efficiency for carbon and nutrients (TN approximate to 72% and TP approximate to 42%) and also in the resistance tests. However, partial disintegration was observed. On the other hand, when ethanol was the substrate, the granules were stable, good nitrogen removal was achieved (TN approximate to 53%), but phosphorus removal was not favored (TP approximate to 31%). Glucose presented the lowest efficiency values for nitrogen (TN approximate to 44%) and phosphorous removal (TP approximate to 21%), and the granules formed (< 1 mm) had the lowest microbial diversity. Therefore, the carbon source had a high impact on the characteristics of the granules.