Postharvest mangoes are prone to anthracnose disease caused by Colletotrichum gloeosporioides. While synthetic fungicides are effective, they pose environmental and health risks. This study introduces a Composite Hydrophobic Nanoemulsion (C-HyDEN) coating, containing fatty acids, terpenes, and polysaccharides, to improve postharvest disease control in fruits. Testing various Hydrophobic Deep Eutectic Solvent (HDES) formulations revealed that a Menthol: Thymol ratio of 1:1 (MT 1:1) was the most effective for the C-HyDEN formulation, with a pH of 6.17 ± 0.04 and the highest radical scavenging activity at 96.23 ± 0.19%. Further formulations, Chitosan + HyDEN and Konjac + HyDEN, were evaluated based on pH, antioxidant activity, viscosity, mean droplet diameter, Polydispersity Index (PDI), zeta potential and Fourier Transform Infrared Spectroscopy (FTIR). Chitosan-HyDEN revealed a pH of 7.21 ± 0.11 and a zeta potential of -30.9 ± 7.5 mV, indicating good stability, and the highest antioxidant activity at 94.27 ± 0.29%. Compared with HyDEN, Antracol^®, and the untreated control, the Chitosan–HyDEN coating extended the shelf life of ‘Harumanis’ mangoes during 21 days of storage (27 ± 2°C; 80% relative humidity), and better-preserved quality attributes, including weight loss, firmness, total soluble solids (TSS), colour, titratable acidity (TA), pH, and DPPH radical scavenging activity. This study suggests Chitosan-HyDEN as a promising, effective alternative to synthetic fungicides for preserving postharvest fruit.