SummaryThe present study demonstrates the first time investigation on Cinnamomum camphora essential oil (CCEO) loaded chitosan nanoemulsion coating on Citrus aurantifolia fruits to ensure protection against Aspergillus flavus infestation and aflatoxin B1 (AFB1) contamination. Encapsulation of CCEO was confirmed through scanning electron microscopy (SEM), X‐ray diffractometry (XRD) and Fourier transform infrared spectroscopy (FTIR). CCEO‐loaded nanoemulsion displayed improved in vitro antifungal (1.0 µL mL−1) and antiaflatoxigenic activity (0.8 µL mL−1) as compared to unencapsulated CCEO. Additionally, CCEO nanoemulsion inhibited synthesis of ergosterol, enhanced the leakage of Ca2+, K+ and Mg2+ ions and retarded methylglyoxal biosynthesis in A. flavus cells. CCEO nanoemulsion coating on C. aurantifolia fruits remarkably reduced weight loss, total soluble solids and titrable acidity along with inhibition of A. flavus contamination and AFB1 secretion during storage. Moreover, nanoemulsion coated fruits maintained the enzymatic antioxidant viz. superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities without affecting sensory attributes, thereby strengthening the practical applicability of CCEO nanoemulsion as nano‐green smart fruit preservative.