Background: Changing climate enhances the survival of pests and pathogens which eventually affects the crop yield and reduces its economic value. To attain the sustainable food security, novel approaches should be employed. Nanobased agri-chemicals provide a distinctive mechanism to increase productivity and manage phytopathogens with minimum environmental distress. In-vitro and greenhouse studies were conducted to evaluate the potential of green synthesized iron oxide nanoparticles (IONPs) in suppressing the wilt infection caused by Fusarium oxysporum f.sp. lycospersici and to improve tomato growth (Solanum lycopersicum) and fruit quality. Results: Various microwave powers (100 W- 1000 W) were used to modulate the properties of green synthesize IONPs by using spinach as a starting material. The IONPs stabilized with black coffee extract were substantively characterized by X-ray diffraction analysis, fourier transform infrared spectroscopy, dielectric and impedance spectroscopy, X-ray photoelectron spectroscopy, Scanning and transmission electron microscopy and magnetization-analysis. XRD revealed cubic magnetite (Fe3O4) phase with superparamagnetic nature, detected at all microwave powers. Binding energies of Fe 2p3/2 (712.05 eV) and Fe 2p1/2 (723.9 eV) of Fe3O4 NPs was confirmed by XPS analysis observed at microwave power of 1000 W. Uniform, spherical shaped particles with an average diameter of 4 nm were confirmed by SEM and TEM analysis. Significant reduction in mycelial growth and spore germination was perceived after exposure to different treatments of IONPs. Malformed mycelium, DNA fragmentation, alternation in cell membrane and ROS production in F. oxysporum indicates antimicrobial affinity of iron oxide NPs. The particles were applied both through root (before transplantation) and foliar application (after two weeks) to infected seedlings. The IONPs significantly reduced the disease severity by an average of 47.8% resulting in increased plant growth variables at exposure to 10 µg/mL of IONPs. Analysis of photosynthetic pigment, phenolic compounds and antioxidant enzymes in root and shoots signifies an increasing trend after exposure to various concentrations of IONPs. Correspondingly, lycopene, vitamin C, total flavonoids and protein content was substantially improved in tomato fruits after treatment of IONPs. Conclusion: These findings of current investigation suggests that IONPs owned antifungal properties to subdue Fusarium wilt disease by boosting plant growth and fruit quality.