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In this study, nanostructured edible coatings based on chitosan nanoparticles (CSNPs) and chitosan‐thyme essential oil nanoparticles (CSTEO‐NPs) were characterized and evaluated on in vitro growth of Colletotrichum gloeosporioides and on inoculated avocado fruit cv. Hass, to evaluate their fungicidal activity and the effect on fruit quality. From TEM and particle size distribution characterization, the size of nanoparticles increased after thyme essential oil incorporation. Overall a synergistic effect between the chitosan and thyme essential oil (TEO) was observed. For in vitro evaluation, incorporation of this essential oil to CSNPs improved the control of C. gloeosporioides as there was a complete growth inhibition. CSNPs with concentrations of TEO at 3 and 5% had a fungicidal effect. The coating formulation with 55% CSTEO‐NPs notably reduced the incidence of C. gloeosporioides on avocado cv. Hass by up to 60%. Also, at the end of the 8‐day storage period, CSTEO‐NPs incorporation into the coating did not affect the quality of avocado; moreover, fruit firmness was better maintained than untreated fruit.