Aflatoxin B1 contamination in the food commodities gains considerable attention due to its mutagenic, carcinogenic, teratogenic, hepatotoxic, and immunosuppressive properties. The study explored the antifungal and aflatoxin B1 inhibitory potential of novel synergistic formulation based on the combination of eugenol, menthol, and t-anethole (EMT) using mixture design assay. The developed formulation (EMT; 1:1:4) exhibited enhanced antimicrobial activity against eleven food-borne molds species and aflatoxin B1 production by Aspergillus flavus (EC-03). Further, the nanoencapsulation of the developed formulation (Ne-EMT) was prepared and characterised by scanning electron microscopy (SEM), x-ray diffraction analysis (XRD), and fourier transform infrared spectroscopy (FTIR). The mechanism of toxicity of Ne-EMT was related to decrease in ergosterol, ions leakage, carbon-source utilization, and impairment in anti-oxidative defence system such as superoxide dismutase (SOD), catalase (CAT), and the ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG) in A. flavus. Molecular docking results showed that the test compounds efficiently interact with targeted genes ver-1 and omt-A (regulatory gene of aflatoxin B1 biosynthesis). Further, Ne-EMT effectively preserved the organoleptic property of the model food system (Eleusine coracana (L.) Gaertn.), strengthens its efficacy as the plant-based antimicrobial agent.