<p>Combining partial nitrification and anammox with denitrifying phosphorus removal (DPR) is considered a promising strategy for nitrogen and phosphorus removal. However, the low nitrate nitrogen availability (produced from anammox) in the side-stream DPR system could affect nutrient removal and the competition between denitrifying phosphate-accumulating organisms (DPAOs) and denitrifying glycogen-accumulating organisms (DGAOs). In this study, the nitrogen and phosphorus removal performance, microbial structure shifts, and key functional groups in a DPR reactor were investigated under long-term nitrate-limited conditions. Over 205&#xa0;days of DPR operation, with the nitrate concentration at the beginning of the anoxic stage gradually decreasing from 15 to 7.5&#xa0;mg/L, stable and efficient nitrogen removal was maintained, while phosphorus removal efficiency reached 96.7 ± 1.6%, despite a reduction in phosphorus release amount. Microbial community analysis revealed that <i>Candidatus_Competibacter</i> became dominated, increasing from 2.3% to 42.2%, which contributed to efficient nitrogen removal. Meanwhile, DPAOs declined to a certain abundance but still maintained phosphorus removal performance. The result indicated that carbon and nitrate availability are the key factors driving microbial succession in the DPR system. Additionally, short-term batch tests demonstrated that the DPR system remained its capability to handle higher nitrate concentrations after long-term nitrate-limited conditions.</p>