The bioavailability of trace metals in soils poses a major threat to the environment, especially with massive mineral fertilizers added to increase plant yield. A plot experiment was conducted for the effectiveness evaluation of compost and vermicompost, recycled from agro-industrial wastes, in immobilizing chromium, cadmium, and lead added to calcareous soil (artificially contaminated). Moreover, immobilization efficiency was compared to the natural occurrence of these metals in the soil without metal addition (uncontaminated soil). In both soils, amendments and mineral fertilizers were applied at three different levels alone and combined to each other. The experimental design was arranged in factorial complete randomized blocks using contamination, organic and mineral fertilizer levels, and their combination as categorical factors. The distribution of metal fractions and their bioavailability in soils and bioaccumulation in wheat grains were evaluated. Soil alkalinity, the contents of soil organic carbon and nitrogen, available phosphorus, and soil micronutrients were significantly improved under vermicompost and compost compared to mineral fertilizer and control. Vermicompost was more effective than compost in reducing metals bioavailability in contaminated soils by increasing the immobilized organic fractions, but it regressed when combined with mineral fertilizers. The bioavailability of the naturally occurring metal levels in uncontaminated soil did not change significantly compared to contaminated soil. Likewise, wheat yield, plant biomass, and nutrient enrichment in wheat grains improved due to enhanced soil nutrient availability. These composted agro-industrial residues, by-products from food industries, can be classified as environmentally-friendly soil amendments for their great potential to enrich soil nutrients, reduce mineral fertilizer addition, enhance plant growth, and stabilize Cr, Cd, and Pb in contaminated calcareous soils under wheat plants.