In-depth research on the side-stream enhanced biological phosphorus removal (S2EBPR) process holds promise for addressing the challenge of low phosphorus (P) enrichment concentration. This study developed a side-stream enhanced biological phosphorus enrichment/removal (S2EBPE/R) reactor by improving a S2EBPR process. The P removal, enrichment, and mass balance were used to evaluate polyphosphate-accumulating organisms (PAOs) activity. Microbial community structures were investigated to reveal the mechanism of P enrichment and stripping. The results showed that the P removal efficiency reached up to 93% in the S2EBPE/R process. Approximately 13% of P-rich liquid could be stably obtained from the side-stream system, with a concentration of 108.85 ± 4.53 mg P/L. Apart from responses to EBPR activity (P/HAc) of up to 0.41 P-mol/C-mol, enrichment of typical PAOs of up to 12.0% enhanced the P enrichment and removal performance. The abundance of functional microorganisms (PAOs and glycogen accumulating organisms (GAOs)) related to P was as high as 13.4%. These findings highlighted the outstanding advantages of the S2EBPE/R process in P enrichment and removal, thereby making significant contributions to P recovery from wastewater.