Sandy soils in tropical areas are more vulnerable to potential toxic elements as a result of their low nutrition. The composite addition of biochar and phosphate material is considered a promising method of immobilizing toxic metals in sandy soils, but the synergistic effects of this process still need to be further explored, especially in typical tropical vegetables. In this study, a pot experiment was conducted to evaluate the agronomic and toxic metal-immobilization effects of single amendments (phosphate rock, activated phosphate rock, and biochar) and combined amendments, including biochar mixed with phosphate rock (BCPR) and biochar mixed with activated phosphate rock (BCAPR), on vegetables grown in tropical sandy soil. Among these amendments, the composite amendment BCAPR was the most effective for increasing Ca, Mg, and P uptake based on water spinach (Ipomoea aquatica L.) and pepper (Capsicum annuum L.), showing increased ratios of 22.5%, 146.0%, and 136.0%, respectively. The SEM-EDS and FTIR analysis verified that the activation process induced by humic acid resulted in the complexation and chelation of the elements P, Ca, and Mg into bioavailable forms. Furthermore, the retention of available nutrition elements was enhanced due to the strong adsorption capacity of the biochar. In terms of cadmium (Cd) and lead (Pb) passivation, the formation of insoluble mineral precipitates reduced the mobility of these metals within the BCAPR treatments, with the maximum level of extractable Cd (86.6%) and Pb (39.2%) reduction being observed in the tropical sandy soil. These results explore the use of sustainable novel cost-effective and highly efficient bi-functional mineral-based soil amendments for metal passivation and plant protection.