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While Mexican lime is an economic tree species, its fruits are prone to postharvest diseases caused by fungal species of the genus Penicillium, which can inflict severe economic loss. To alleviate these adverse effects, there has been a rise in interest for environmentally-friendly treatments in the fruit industry due to consumers' concern for food safety. Here, thyme (Thymus vulgaris) essential oil (TEO) (0.2%) and carboxy methyl cellulose (CMC) coating (1.5%) were evaluated for in vitro and in vivo activities against green and blue molds on Mexican lime. Using a combination of TEO and CMC led to the highest antifungal activity in vitro. Moreover, a decrease in disease incidence and severity was observed in vivo when Mexican lime fruits were treated with either TEO (0.2%) or CMC (1.5%). The results of scanning electron microscopy (SEM) showed that CMC + TEO caused changes in the morphology of both P. digitatumand P. italicumhyphae, resulting in non-linear and wrinkled surfaces. Therefore, a combination of TEO and CMC can be used as an effective treatment for green and blue mold on Mexican lime.