In this study, an advanced wastewater treatment process, the denitrifying phosphorus/side stream phosphorus removal system (DPR-Phostrip), was developed for the purpose of enhancing denitrifying phosphorus removal. The enrichment of denitrifying phosphorus-accumulating organisms (DPAOs) and the microbial community structure of DPR-Phostrip were evaluated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and the metabolic activity of seed sludge and activated sludge collected after 55 days of operation were evaluated by Biolog™ analysis. This experimental study of DPR-Phostrip operation showed that nutrients were removed effectively, and denitrifying phosphorus removal was observed during the pre-anoxic period. PCR-DGGE analysis indicated that DPR-Phostrip supported DPAO growth while inhibiting PAOs and GAOs. The major dominant species in DPR-Phostrip were Bacteroidetes bacterium, Saprospiraceae bacterium, and Chloroflexi bacterium. Moreover, the functional diversity indices calculated on the basis of Biolog analysis indicated that DPR-Phostrip had almost no effect on microbial community diversity but was associated with a shift in the dominant species, which confirms the results of the PCR-DGGE analysis. The results for average well color development, calculated via Biolog analysis, showed that DPR-Phostrip had a little impact on the metabolic activity of sludge. Further principal component analysis suggested that the ability to utilize low-molecular-weight organic compounds was reduced in DPR-Phostrip.