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Rhizoctonia solani Kühn and Sclerotium rolfsii Sacc. are the primary soil-borne plant diseases responsible for significant reductions in global crop yields. The primary goal of this study was to investigate the antifungal potentials of clove essential oil (CEO), nanoemulsion form (CEONE) and chitosan/nanoemulsion nanocomposite (CS/CEONE) against R. solani and S. rolfsii through in vitro and in vivo trials. Both CEONE and CS/CEONE were prepared and investigated for their physical chemical and morphological characterization. The poisoned medium method was utilized to evaluate the inhibitory effects of CEO, CEONE and CS/CEONE on the mycelial growth and enzymatic activity of R. solani and S. rolfsii. The changes of hyphae of R. solani and S. rolfsii in response to treating with CEONE and CS/CEONE were observed with scanning electron microscope (SEM). The results revealed that CEONE have larger size 86 ± 3 nm and a broader range of PDI 0.121 ± 0.011 on the average. While, CS/CEONE has smaller size of 49 ± 4 nm and narrower PDI of 0.099 ± 0.009. Both nanoemulsions had uniform spherical nanodroplets form and exhibited acidic nature. Fourier Transform Infrared Spectroscopy (FTIR) and UV-Visible Spectroscopy (UV-Vis) verified the successful incorporation of both CS and CEO within the nanoemulsion system. The results demonstrated a sustained and prolonged release profile from CS/CEONE for up to 4 days. The inhibitory effect of CEONE and CS/CEONE showed dose-dependent activity against mycelial growth of both fungi. CEONE and CS/CEONE at concentration 500 µL/L exhibited the strongest inhibition with a significant (p < 0.05) variation among them with value ranging from 56.11% to 71.94% and 52.2% to 79.2%, respectively. Comparing to control, CS/CEONE revealed the highest inhibitory effect against S. rolfsii after 96 h followed by CEONE with value reached 50.6% and 44.1%, respectively. The antifungal activity of the nanoemulsion showed strain–dependent behavior, where S. rolfsii was the most affected. SEM images showed changes in the hyphal structure of S. rolfsii and R. solani resulting from the impact of CEONE and CS/CEONE. Activity of pectinase and cellulase secreted by both fungi was also negatively affected by CEO, CEONE and CS/CEONE at all tested concentrations. Greenhouse trials revealed that increasing the concentrations of CEO, CEONE, and CS/CEONE from 50 to 500 μL/L gradually increased their effectiveness in reducing the DI% and DS% of black scurf, stem canker, pre-damping off, and post-damping off diseases on potato. The results suggest that incorporation of CS to CEONE enhanced its activity and can be utilized as a secure and non-toxic nanocomposite. Supplementary Material Supplementary Material File [ABSTRACT FROM AUTHOR]