There is an increasing interest in developing natural methods to replace the current chemicals used for maintaining postharvest quality of citrus fruits. The essential oil antifungal activity of mint (MEO), basil (BEO), and lavender (LEO) acting as the vapor-phases was tested against Penicillium digitatum. The minimum doses with fungistatic and fungicidal effect, in vitro, acting as the vapor-phases, were set up. The minimum fungicidal dose was 300 μL for BEO and 350 μL LEO, while for MEO only minimal dose with fungistatic effect was reached. The IC50 values were calculated and used (v/v) for testing preservation of lemon fruits, in close space enriched in vapor oil. For this purpose, the following two independent in vivo experiments were carried out: experiment 1, inoculated lemons with P. digitatum stored without chemical treatments 7 days, at 22 ± 2 °C, at two concentrations (C1—IC50 equivalent; C2—half of C1); and experiment 2, the non-inoculated lemons kept under the same conditions and concentrations of EO vapor served to evaluate the lemon quality properties. The results showed that antifungal protective effect was provided in the order of LEO-C1 > BEO-C1 > MEO-C1 > BEO-C2 > MEO-C2 > LEO-C2. The quality indicators like weight loss, pH, and firmness were not negatively influenced.