The leachate of waste phosphogypsum (PG) contains substantial amounts of phosphate, sulfate, and fluoride, which poses an immense threat to the safety of the aquatic ecosystem. In this study, a multi-stage precipitation approach is proposed to treat PG leachates using hybrid alkaline reagents including barium hydroxide (Ba(OH)2) and quicklime (CaO). To avoid potential environmental impacts, hazardous environmental contaminants are removed from the PG leachates by adding alkaline reagents in a specific order. The multi-stage precipitation approach achieves nearly 100% removal efficiencies for phosphate, fluoride, and metal ions as well as satisfactory removal efficiencies for sulfate and ammonia nitrogen (93.6% and 94.8% respectively). The compositions of generated mineral precipitates are comprehensively investigated by analytical techniques including X-ray diffraction (XRD), transmission electron microscope (TEM), etc. The main precipitated mineral phases are barite (BaSO4), brushite (CaHPO4·2H2O), and hydroxyapatite (Ca5(PO4)3OH). This is further proven by the geochemical modeling using Visual MINTEQ, in which the precipitation of mineral phases is calculated. Furthermore, a straightforward economic analysis indicates the proposed method has a lower cost of the use of alkaline reagents. Overall, this study establishes an effective and eco-friendly approach for the treatment of waste PG leachates to remove hazardous environmental contaminants and recover valuable precipitates.