The present study evaluated the phytoremediation activities of Populus alba upon using nano metal-based-oxides (i.e., Fe2O3, ZnO, and Mn2O3-NPs) as analogues of three main heavy metals Fe, Zn and Mn exist in soil as micronutrients at three different concentrations (i.e., 20, 40, and 60 mg/L) compared to the control. The as-prepared nanoparticles have been prepared via co-precipitation method. In addition, the physico-chemical properties were investigated using transmission electron microscopy, Fourier transform infrared spectra, X-ray diffraction and dynamic light scattering techniques. Overall, a significant difference in the biomass production-related parameters such as fresh weight, shoot length, root length, and root number compared to control upon the treatment with micronutrients-based nano-metal-oxides (i.e., Mn2O3 > Fe2O3 > ZnO NPs, respectively), except a significant increase in the root number of Populus alba plant upon their treatment with ZnO NPs compared to other prepared nano-metal-oxides and control. Also, a remarkable increase in the chlorophyll index was monitored upon treatment with Fe2O3 than other used Mn2O3 and ZnO NPs, respectively. Moreover, RAPD-PCR bioassays were applied and the actual 6 primers showed a genetic variation percentage of 34.17% indicating that Populus alba is highly genetically stable even in a highly contaminated environment/soil. All these data enhance the idea of using the Populus alba plant in phytoremediation and heavy metal uptake as micronutrients to clean up the surroundings.