Infection of rice grains in the field during harvest and storage by Aspergillus flavus, a toxigenic mold causes significant losses to market acceptability of seeds due to its detrimental effects on seed health and quality parameters. Production of aflatoxin by A. flavus interferes with physiological factors affecting the quality of seeds during storage in addition to nutritional losses to the grains. Chemical seed treatments are generally not recommended during storage due to their adverse effects on seed germination and vigor. Leaves of the neem tree (Azadirachta indica) are well known for antifungal properties against phytopathogenic fungi such as A. flavus. The paper presents the effect of neem leaf extract adsorbed onto sodium alumino-silicate (SAS) nanoparticles against A. flavus in rice seeds during storage. SAS-Neem nanocomposite, a novel unexplored seed storage material against toxigenic A. flavus, was synthesized for augmented antitoxin and seed invigorating potential. The nanocomposite was characterized using an array of microscopic and spectroscopic methods to evaluate the adsorption of neem leaf extract components on SAS nanoparticles. The antifungal mechanism of the nanocomposite was evaluated via scanning electron microscope, phase contrast, and fluorescence microscopy. The toxin analysis of pathogen-inoculated seeds was carried out at monthly intervals for 6 months during storage of two rice varieties, i.e. PR114 and Pusa-Basmati 1121. The results indicated that the nSAS-Neem composite used as seed coating material maintained significantly higher seed germination (86.23 and 81.49%) and minimized seed rot (6.70 and 5.30%, respectively) in the two varieties under study than the control after 6 months of storage. There was a notable decrease in toxin concentration from 20.58 to 11.19 μg/kg and 19.16 to 12.58 μg/kg in seeds of the two varieties i.e. PR114 and Pusa Basmati 1121, respectively. The nano-composite proved effective against toxigenic A. flavus during seed storage of rice without compromising the seed quality parameters.