•MgONPs were synthesized through green approach using trichoderma fungus.•Myco-synthesized NPs exhibited strong nematicidal activity.•Soil application of NPs improved plant growth under nematode infection.•Soil application of NPs reduced nematode population and development. Meloidogyne incognita is believed to be the most devastating pest causing severe damage to crops, and hence, innovative and effective means of controlling the nematode is the need of the day. The focus of the current study is to devise an effective and innovative myco-fabrication of MgO nanoparticles (NPs) along with melatonin for efficient management of M. incognita infecting tomatoes. Fungal extracts were used to synthesize the myco-fabricated NPs through a green synthesis pathway and were verified using different spectroscopic means. The nanoparticles exhibited appreciable nematicidal potential, such as drastic egg hatch inhibition and juvenile mortality under in vitro assays. Evaluation of NPs and melatonin in planta, alone or combined form, was investigated on tomato plants already inoculated with M. incognita. The alterations in the nematode population on roots of plants as well as in soil, growth parameters, and biochemical attributes of plants were recorded. A significant reduction in nematode population was revealed on the application of melatonin and myco-fabricated nanoparticles, hence exhibiting an improvement in the plant's biochemical (glutathione, phenolic, flavonoid, and antioxidant enzymes) and growth parameters. A synergistic impact was shown on the combined application of the treatments. Furthermore, an enhancement in the expression as well as activities of antioxidant enzymes was also observed. Increased resistance of plants against nematodes resulted in connection with the improved antioxidant status of plants due to this combined treatment. The significantly improved growth of plants under M. incognita stress conditions reveals the potential of the proposed treatments having synergistic interaction to manage phyto-parasitic nematodes effectively. This presents innovative means of agricultural biotechnologies that have the potential to contribute to the efficient management of nematodes infecting plants.