Aerobic granular sludge (AGS) is an emerging technology offering an alternative wastewater treatment with a reduced footprint compared to conventional activated sludge systems. Basic understanding of AGS processes has mainly been obtained in laboratory-scale studies with simple synthetic wastewaters containing volatile fatty acids (VFA) as main carbon sources. Yet, the bacterial communities of AGS treating municipal wastewater have been much less investigated. Two approaches were applied here to assess the impact of fermentable and polymeric compounds on the microbial communities of the AGS and thus make a step toward the comprehension of AGS systems treating municipal wastewater. The first approach was to run an AGS reactor with a simple synthetic wastewater containing VFA as carbon sources and to make a progressive transition to a complex synthetic wastewater, by adding fermentable and polymeric compounds. The bacterial communities of weekly samples were monitored by 16S rRNA gene amplicon sequencing. The second approach was to start in parallel four AGS reactors fed with distinct wastewaters with activated sludge as inoculum. Two reactors were fed with the two synthetic wastewaters used in the first approach, the simple and complex synthetic wastewaters. The other two reactors were fed with either primary clarifier effluent or raw municipal wastewater. In both experiments, the microbial community from the AGS treating simple synthetic wastewater was clearly different from the one treating complex synthetic wastewater. Similarities within the microbial communities fed with the same carbon source were identified. Interestingly the synthetic complex wastewater led to a bacterial community which was closer to the one obtained in the reactors treating real wastewaters. The results of this study show that the type of carbon source is a major factor shaping the bacterial community structure of AGS and that by working with simple synthetic wastewater, one may bacteria which play an important role in the treatment of municipal wastewater. The use of a complex synthetic wastewater may provide a more appropriate model system for the study of the bacterial communities in AGS.