Lemon postharvest losses are mainly due to the presence of fungal diseases. Current postharvest decay strategies rely on synthetic chemical fungicides; however, consumers are demanding that fruit is free of any chemical residue. The use of new natural alternatives, including essential oils, is emerging due to their potential antimicrobial activity. Therefore, the aim of this work is the elucidation of the effect of carvacrol, eugenol, and thymol, individually and in combination, applied in preharvest. Three different concentrations (100, 500, and 1000 µL/mL) of carvacrol, eugenol, and thymol were individually applied and in combination in ‘Fino’ and ‘Verna’ lemon cultivars. The fungal incidence (mainly Penicillium digitatum and P. italicum) was evaluated weekly for 35 days. Moreover, the main different quality parameters (weight loss, firmness, colour, total soluble solids, titratable acidity, and total phenolic content) of lemons were evaluated at harvest and after 35 days of cold storage. The results showed that carvacrol at the lowest concentration (100 µL/L) provided the lowest fungal incidence with a non-negative effect on the lemon quality parameters during storage, while the highest concentrations and the combination of essential oils resulted in the opposite effect. Therefore, carvacrol applied at 100 µL/L in preharvest could be an eco-friendly alternative to the current fungicides to control lemon decay, while maintaining their optimal quality.