The present study focuses on the facile green synthesis of magnetic nanoparticles (MNPs) using onion waste of Allium Cepa L. (MNP@OW) for effective removal of noxious mercury from simulated wastewater. Photogenically synthesized MNPs were functionalized with DL-homocysteine (HC@SiO2@MNP@OW) for selective mercury adsorption. Various characterization techniques were employed to confirm their physical properties. Vibrating sample magnetometer (VSM) studies indicated MNP@OW’s superparamagnetic nature with a saturation magnetization (Ms) of 48.35 emu/g, while HC@SiO2@MNP@OW had a reduced Ms of 4.52 emu/g due to a coating of non-magnetic silica and DL-homocysteine. Both adsorbents showed optimal adsorption at 80°C and pH 8. However, it is explicitly mentioned that HC@SiO2@MNP@OW demonstrated efficient mercury removal at a lower dosage and shorter contact time compared to MNP@OW. Fast separation times of 6 and 26 seconds for MNP@OW and HC@SiO2@MNP@OW, respectively, confirm their ease of separation from simulated wastewater. The Freundlich isotherm model fit the data well and kinetic analysis supported a pseudo-second-order model, revealing a chemisorption mechanism. Moreover, HC@SiO2@MNP@OW demonstrated high selectivity, even in the presence of co-existing ions. Green synthesized MNP@OW and HC@SiO2@MNP@OW exhibited promising potential as low-cost sorbents for efficient mercury removal from simulated wastewater, making them feasible for wastewater treatment in low-economic countries.