Chemical seed treatments are often applied to soybeans to protect the seedling from early season pathogens, and thus extend the plant's growing cycle and increase yield. However, under organic and sustainable production systems chemical treatments are restricted and planting date has to be delayed. Natural seed treatments based on plant-made essential oils are a viable alternative in other crops, but little is known about their effectiveness in controlling soybean seed and soil borne pathogens. The objectives of this study were to screen plant essential oils for their antimicrobial properties using seed and soil borne model pathogens, to determine the minimum inhibitory concentration (MIC) in vitro and to test in vitro and in vivo antimicrobial efficacy on seed. Antifungal and antibacterial properties of the essential oils of anise, basil, bay, black pepper, caraway, cinnamon, clove, coriander, lavender, lemongrass, nutmeg, oregano, peppermint, rosemary, sage, savory, tea tree and thyme were tested against three soybean pathogens: Phomopsis sp., Pseudomonas syringae pv. glycinea and Pythium sp. Results from in vitro experiments showed that cinnamon, clove, oregano and savory essential oils controlled Phomopsis at MIC of 400 ppm. Cinnamon, clove, lemongrass and oregano controlled Pythium at MIC of 200 ppm. Oregano and savory controlled Pseudomonas at MIC of 400 ppm. Seed germination was unaffected by the application of the essential oils at their MIC.