In South Asia, the high costs of synthetic fertilizers have imposed research on alternative nutrient inputs. We aimed to identify potential trace elements (PTE) present in some organic manure that might be a source of environmental pollutions and risk to public health following consumption. The study aims to evaluate how different organic waste (poultry waste, PW; press mud, PM; and farmyard manure, FYM) influences the heavy metal migration in soil, the accumulation in garlic, and their potential health risks. Organic waste caused a higher accumulation of certain metals (Zn, Cu, Fe, and Co), whereas Mn, Cd, Cr, and Pb were in lower concentrations in soil. Amendments of soil with PM revealed a higher accumulation of Cd, Cr, Fe, and Pb, whereas PW resulted in Cu and Zn accumulation in garlic. Treatment of soil with FYM exhibited higher metal concentration of Co and Mn. An environmental hazard indices study revealed that pollution load index (PLI) was highest for Cu following treatment with PM. The health risk index (HRI) was greater for Cd following amendment with PM. Maximum daily intake of metals (DIM) was observed for Zn after treatment with PW. The Pb exhibited maximum bioconcentration factor (BCF) in PM-amended plants. Based on these findings, we concluded that garlic grown on contaminated soil with organic waste may pose serious health hazards following consumption.