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The main objective of this study is to evaluate the effect of selected essential oils thyme chemotype linalool (<i>Thymus zygis</i> L.), thyme chemotype tymol (<i>Thymus vulgaris</i> L.), eucalyptus <i>(</i><i>Eucalyptus globulus</i> Labill.), lavender (<i>Lavandula angustifolia</i> Mill.), mint (<i>Mentha piperita</i> L.), almond (<i>Prunbus dulcis</i> Mill.), cinnamon bark (<i>Cinnamomum zeylanicum</i> Nees), litsea (<i>Litsea cubeba</i> Lour. Pers), lemongrass (<i>Cympogon citrati</i> L. Stapf), and ginger <i>(Zingiber officinalis</i> Rosc.) in the vapor phase on growth, sporulation, and mycotoxins production of two <i>Aspergillus</i> strains (<i>Aspergillus parasiticus</i> CGC34 and <i>Aspergillus ochraceus</i> CGC87), important postharvest pathogens of green and roasted coffee beans. Moreover, the effect of the essential oils (EOs) on the sensory profile of the coffee samples treated with EOs was evaluated. The major components of tested EOs were determined by gas chromatography and mass spectrometry (GC–MS) and gas chromatography with flame ionization detector (GC-FID). The results showed that almond, cinnamon bark, lemongrass, and litsea EOs are able to significantly inhibit the growth, sporulation, and mycotoxins production by toxigenic fungi. Sensory evaluation of coffee beans treated with EOs before and after roasting showed that some EOs (except lemongrass and litsea) do not adversely affect the taste and aroma of coffee beverages. Thus, application of the vapors of almond and cinnamon EOs appears to be an effective way that could serve to protect coffee during its transport and storage from toxigenic fungi.