To meet the United Nations’ Sustainable Development Goals, agricultural soil which is a non-renewable natural resource must be carefully managed. Heavy metals present in agricultural soil may imperil food security and instigate extreme risks to human health. Organic wastes have been long known for valuable amendments to soil thereby, improving overall soil health. In the present study, Echhornia crassipes, Hydrilla verticillata, and vegetable waste, was utilized to prepare compost amendments. Lycopersicum esculentum was used to metal uptake from compost amended soils. 5%, 10%, 15%, 25%, and 35% compost: soil (w/w) were studied to understand metal translocation in plants. Potential Ecological risk indices showed that while the degree of risk was medium for the natural soil, it reduced to slight for the soil amended with WHC and VWC for all compositions. The non-carcinogenic risks associated with the human health reduced on application of the composts, however, they still remained substantial for Fe, As, and Pb for WHC, HVC, and VWC composts at higher application ratios, especially among children. On the other hand, the carcinogenic health index values which were calculated to estimate the risk associated with ingestion of L. esculentum, showed a decrease in risk for all the metals studied, upon soil amendment. Soil amended with HVC compost showed an increase in carcinogenic risk for As, Pb, and Cr. Finally, we conclude that biological soil remediation is economical and a sustainable land management strategy that may lead to green and clean remediation solutions for metal contaminated soil.