Landfilling is common in developing countries since it is the easiest and cheapest way of waste disposal, however, it leads to serious environmental problems such as soil, water, and air pollution. A landfill has a life span of fifteen years after which it is closed leaving the site unusable, as a result, effective methods are needed for restoring and reclaiming the closed landfill site for future use. Phytoremediation has emerged as a viable and environmentally friendly method, which uses green plants to remove pollutants from soil, air, and water. In this study, Medicago sativa (alfalfa) and Trifolium repens (white clover) were planted in a pot trial as monocropped and intercropped in polluted soil collected from a landfill site to investigate stress tolerance and the extent of bioaccumulation of Cr, Mn, Ni, and Zn. All the plants remained healthy throughout the trial, with no signs of phytotoxicity except for monocropped white clover plants that showed stunted growth and eventually died. Intercropping resulted in the reduction of metals and their toxic effects in the soil which in turn limited the uptake of metals by both plants as a defence strategy against metal stress which resulted in lower amounts of metals in the intercropped plants compared to monocropped plants. The roots absorbed a significant amount of Zinc (Zn), Nickel (Ni), and Manganese (Mn) in the roots than the leaves. The concentration of Chromium (Cr) was significantly higher than the other metals in all the plants and there was no significant difference in the concentration of Cr in the roots and leaves. The Scanning Electron Microscopy (SEM) chromatographs, revealed greater damage in the tissues of monocropped plants than the intercropped plants, demonstrating that inter- cropping enhances plant growth and development by reducing the toxic effects of biotic stress such as metals in the soil than monocropping. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) revealed flavonoids as the main secondary metabolites that promoted resilience to biotic and abiotic stressors in Trifolium repens while saponins were found to play a similar major role in Medicago sativa.