Global warming, pollution problems, and the demand for sustainable food production forced farmers to find new solutions for biological plant protection. Usage of natural renewable sources around us seems to be an alternative. Compounds isolated from other plants and distinguished with antifungal properties can be used to protect vegetables from the seed-borne pathogens. The study aimed to elucidate the ability of essential oils of Juniperus communis L., Hyssopus officinalis L. and Thymus vulgaris L. to control carrot seed-borne pathogen Alternaria spp. The agar-plate method was used for carrot seeds infestation with micromycetes. Essential oils extracted from common juniper, hyssop and thyme, then separately mixed with potato dextrose agar media at different concentrations and the antifungal activity of each oil tested in vitro. The results revealed that the T. vulgaris essential oil (200–1000 μL L-1) significantly inhibited Alternaria spp. growth. The H. officinalis essential oil even promoted seed damage the second and fifth day of the evaluation compared to control; however, the concentration of 400 μL L-1 showed little suppression of micromycete development 7 days after inoculation. In vitro experiments indicated that 600 μL L-1 of J. communis essential oil could control seed-borne pathogen viability. Overall, thyme essential oil expressed a high potential for application in biofungicides formulations.