Bioelectrochemical systems (BESs) have been acknowledged to be an efficient technology for refractory pollution treatment. An electron donor is as an indispensable element of BES, and domestic wastewater (DW) has been proved as a cost-efficient and accessible alternative option to expensive carbon sources (such as acetate and glucose), yet its effect on microbial community evolution has not been thoroughly revealed. In this study, the electrode microbial communities from BESs treating azo dye wastewater fed by DW (R_DW), acetate (R_Ac), and glucose (R_Glu) were systematically revealed based on 16S rRNA Illumina MiSeq sequencing platform. It was found that there were significant differences between three groups in microbial community structures. Desulfovibrio, Acinetobacter, and Klebsiella were identified as the predominant bacterial genera in R_DW, R_Ac, and R_Glu, respectively. Methanosaeta, the most enriched methanogen in all reactors, had a relative lower abundance in R_DW. Microbial communities in R_Ac and R_Glu were sensitive to electrode polarity while R_DW was sensitive to electrode position_. Compared with pure substrates, DW increased the diversity of microbial community and, thus, may enhance the stability of electrode biofilm. This study provides an insight into the microbial response mechanism to the electron donors and provides engineering implications for the development of BES.