Copper (Cu) and zinc (Zn), two potentially toxic trace elements, are commonly abundant in organic wastes (OWs) recycled in soils as fertilizer. Yet current knowledge on the long-term behavior and fate of Cu and Zn in soil following OW spreading is scant. We addressed this issue by studying the fate of OW-borne Cu and Zn in amended soils from four different long-term field experiments. By combining the stable isotope analysis and X-ray absorption spectroscopy, we identified changes in Cu and Zn concentrations, speciation and isotopic compositions in the amended soils only when OW had been applied at high rates over long periods. Under these conditions, we highlighted that: (i) all OW-derived Cu and Zn had accumulated in the topsoil layer regardless of the soil and OW type; (ii) the amended soil isotopic signatures were the result of the mixing of OW-borne and natural Cu and Zn; and (iii) Cu and Zn exhibited distinct speciation patterns in amended soils. Indeed, the unprecedented persistence of OW-borne crystallized Cu(I)-sulfide in the amended soils contrasted with the complete transformation of pig slurry-borne nanosized Zn-sulfide or household compost-derived amorphous Zn phosphate and Zn complexed by organic matter.