Side-stream EBPR process (S2EBPR) is a new alternative to address the common challenges in EBPR related to weak wastewater influent and to improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure between four S2EBPR with conventional EBPR configurations in US was conducted. The statistical analysis suggested higher performance stability in S2EBPR than the conventional EBPRs, although possible bias is recognized due to variations in the target permit levels and plant-specific factors among the plants. Total and known PAOs and GAOs abundance and identities were investigated with FISH, DAPI, 16S rRNA gene sequencing and Raman microspectroscopy. The results suggested comparable relative PAO and Candidatus Accumulibacter abundances in S2EBPR and conventional EBPR systems. Tetrasphaera, a putative PAO, was also found at similar abundance in S2EBPR as in conventional facilities, whereas the relative abundance of known GAOs was lower in S2EBPR than those typically seen at conventional EBPRs. Microbial community analyses via 16S rRNA gene amplicon sequencing revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional plants. Shannon and Inverse Simpson indices, which are combined measures of richness and evenness evaluation of the microbial communities, suggested that the microbial diversity in S2EBPR plants were higher than those in conventional EBPRs.