The chemical composition of commercial Syzygium aromaticum, Cinnamomum verum, and Laurus nobilis essential oils as well as their antifungal activity against four pathogenic fungi isolated from Mediterranean rice grains has been investigated. Eighty nine compounds accounting for between 98.5 and 99.4% of the total essential oil were identified. The phenylpropanoids eugenol (89.37 ± 0.29%) and eugenol (56.34 ± 0.41%), followed by eugenol acetate (19.48 ± 0.13%) were, respectively, the main compounds in clove and cinnamon essential oils, whereas large amounts of the oxygenated monoterpenes 1,8-cineole (58.07 ± 0.83%) and α-terpinyl acetate (13.05 ± 0.44%) were found in bay leaf essential oil. Clove and cinnamon oils showed the best antifungal activity results against all tested fungi. Against Alternaria alternata, clove essential oil displayed the best antifungal effect, whereas against Curvularia hawaiiensis, cinnamon essential oil was more active. Both essential oils showed a similar antifungal effect towards Fusarium proliferatum and Fusarium oxysporum. In vitro studies in inoculated rice grains showed that clove and cinnamon totally inhibited pathogenic fungal development after 30 days of incubation. In vivo studies showed that eugenol used with a polysaccharide such as agar-agar formed a fine coat which wraps the inoculated rice grains, creating a natural biofilm and reducing the development of all pathogenic fungi (80-95%) for 30 days.