In this study, phosphate-rich supernatant at the end of anaerobic phase was extracted by a certain side-stream ratio for chemical precipitation to investigate the optimal conditions for phosphorus recovery. The effect of side-stream reaction on the performance of the mainstream Enhanced Biological Phosphorus Removal (EBPR) system was also explored. The experiment was carried out in a sequencing batch reactor (SBR) operated in an alternating anaerobic/aerobic mode with dissolved oxygen controlled at 1.0 mg · L−1. The results showed that the optimum magnesium source,temperature, stirring speed and reaction equilibrium time for side-stream phosphorus recovery were: MgCl2 · 6H2O, 25 °C, 150 rpm and 20 min, respectively. It was also observed that the average phosphorus removal efficiency of the mainstream system maintained as high as 90.7% during the side-stream extraction period despite insufficient time for phosphate uptake under limited dissolved oxygen condition and phosphate deprivation of polyphosphate-accumulating organisms (PAOs). Besides, the sludge settling performance of the mainstream EBPR system decreased with no sludge loss. Afterwards, phosphorus removal and sludge settling performance were restored with dismissing side-stream phosphorus recovery. This study suggested that side-stream extraction of anaerobic supernatant from a mainstream EBPR subjected to low dissolved oxygen conditions for chemical phosphorus recovery was feasible and environmentally friendly.