Fungal deterioration is a recurring problem in citrus fruits, and the search for natural preservatives has been widely publicised. Therefore, the in vitro antifungal activity of clove, white thyme, tea tree, Eucalyptus citriodora, Eucalyptus staigeriana, green mandarin, sicilian lemon, sweet orange, and bergamot essential oils (EO’s) was evaluated against the mycelial growth of Penicillium digitatum isolated from contaminated citrus fruits, by direct contact and volatiles action. In addition, the chemical composition and volatile compounds of the EO’s were evaluated by gas chromatography. Clove, white thyme, and Eucalyptus citriodora EO’s inhibited 100% of the mycelial growth of P. digitatum by direct contact and volatile action at concentrations ≤ 2 µL/mL. On the other hand, EO’s from citrus sources could not inhibit 100% of mycelial growth by any mechanism of action. Thus, the clove, thyme, and Eucalyptus citriodora EO’s are promising for developing new ecologically correct products for controlling phytopathogens in citrus fruits.