Bell pepper presents rapid weight loss and is highly susceptible to gray mold caused by the fungus Botrytis cinerea. The most employed method to control this disease is the application of synthetic fungicides such as thiabendazole (TBZ); however, its continued use causes resistance in fungi as well as environmental problems. For these reasons, natural alternatives arise as a more striking option. Currently, bell pepper fruits are coated with carnauba wax (CW) to prevent weight loss and improve appearance. Moreover, CW can be used as a carrier to incorporate essential oils, and previous studies have shown that thyme essential oil (TEO) is highly effective against B. cinerea. Therefore, this study aimed to evaluate the effect of CW combined with TEO on the development of gray mold and maintenance of microestructural and postharvest quality in bell pepper stored at 13°C. The minimal inhibitory concentration of TEO was 0.5%. TEO and TBZ provoked the leakage of intracellular components. TEO and CW+TEO treatments were equally effective to inhibit the development of gray mold. On the quality parameters, firmness and weight loss were ameliorated with CW and CW+TEO treatments; whereas lightness increased in these treatments. The structural analysis showed that CW+TEO treatment maintained the cell structure reducing the apparition of deformities. The results suggest that CW+TEO treatment could be used as a natural and effective antifungal retarding the appearance of gray mold and maintaining the postharvest quality of bell pepper. PRACTICAL APPLICATION: CW and TEO are classified as generally recognized as safe (GRAS) by the US Food and Drug Administration (FDA). This combination can be employed on the bell pepper packaging system to extend shelf life and oppose gray mold developments. Bell pepper fruits are normally coated with lipid-base coatings such as CW before commercialization; therefore, TEO addition would represent a small investment without any changes on the packaging system infrastructure.