Phytoextraction is an environmentally friendly and potentially cost-effective technique to remove toxic elements from contaminated soil. Lower biomass production of hyper-accumulator plants is a major bottleneck of the phytoextraction process. A pot experiment was conducted to explore three accumulator plants namely sunflower, marigold, and spinach for their phytoextraction ability in zinc (Zn) and copper (Cu) contaminated soil, and to study their effect on distribution of the metals on different soil solid fractions. Our study demonstrated the effect of growing accumulator plants on distribution of Zn and Cu in various soil-solid phases after phytoextraction process. The efficiency of phytoextraction was compared in terms of the metal uptake ability of the accumulator plants. The order of accumulator plants based on phytoextraction of Zn follows sunflower > marigold = spinach, whereas order of Cu uptake followed as sunflower > marigold > spinach. Fractionation study showed that in sunflower and marigold grown soil, dissolved carbonate bound fraction of Zn enriched water-soluble and exchangeable fraction of Zn, while in spinach grown soil, the dissolved carbonate bound fraction of Zn enriched the organically bound fraction. Thus, it can be inferred that sunflower and marigold increased the bioavailability and toxicity of Zn and Cu more than that of spinach did. The outcome of the study is sunflower is superior to marigold and spinach as far as phytoextraction of Zn and Cu contaminated soil is concerned.