Side-stream Enhanced biological phosphorus removal (S2EBPR) has been incorporated with the B-stage process to enable simultaneous phosphorus and nitrogen removal. However, the dominating phosphorus accumulating organisms (PAOs) in this novel configuration has not been evaluated. The dominance ofAcinetobacterwas confirmed by 16S sequencing. In addition, single-cell Raman spectrum (SCRS) analysis in couple within situfluorescence in situ hybridization (FISH) was applied to obtain the feature spectrum and verify the phosphorus release/uptake activity of Acinetobacter spp. The phenotypic profiling further suggested the dominance ofAcinetobacter-like organisms among all poly-phosphorus containing organisms and only certain phenotypicAcinetobacter(oligotype 1) contribution to P-removal in a unique HRAS-P(D)N-S2EBPR system. The findings suggest thatAcinetobactermay outcompete other heterotrophic organisms in EBPR systems due to their sensitivity to operational conditions. However, stable P-removal was only observed during a specific section of the operation period, coinciding with an increase in the VFA/P ratio. Further research is needed to identify the phenotypes of Acinetobacter responsible for P-removal in EBPR systems. The study contributes to a better understanding of the microbial ecology and engineering aspects of EBPR systems and wastewater treatment in general.