This research aims to address common constraints in the effective utilization of plant nutrients in soil, such as fixation, mobility, leaching, and reactions with soil colloids. To mitigate these issues, Fe and Zn citrate nanoparticles were synthesized and applied as nanochelators in a reconstructed soil profile column. We evaluated the mobility, release, and leaching behaviors of these nanoparticles. Results revealed that, no leaching of Fe and Zn citrate nanoparticles occurred even after a 90-day incubation. The release profiles exhibited a peak at 60 and 90 days for Fe and Zn respectively. In the mobility studies, Fe and Zn availability was highest in the 0–15 cm soil depth. Fe citrate and Zn citrate nanoparticles demonstrated the highest availability at 264.7 mg/kg and 86.26 mg/kg of soil, respectively as compared with commercial samples. The superior performance of Fe and Zn citrate nanoparticles was observed in terms of reduced leaching and improved accessibility, indicating their potential as efficient and environmentally-friendly plant nutrient sources. The study concludes that Fe and Zn citrate nanoparticles are stable nutrient sources that can enhance plant use efficiency with minimal environmental impact.