The purpose of this study was to estimate the efficacy of 2% baking soda (sodium bicarbonate) and ultra-sonication on the fungi and bacteria disinfection and germination of organic vegetable seeds. The predominant fungi and bacterium were Altanaria sp. and Pseudomonas sp. in organic vegetable seeds. The treatment of 2% baking soda alone showed low germination rate of organic root, leafy vegetable and cucurbit seeds, but the germination and disinfection efficacy was increased by the combined treatment with 2% baking soda and ultra-sonication. Among the vegetable seeds, Radish, turnip, Chinese cabbage, and cabbage treated with 2% baking soda and ultra-sonication for one minute had the highest disinfection and germination efficacy. Also, beet, melon and watermelon were the highest disinfection and germination efficiency for 2 minutes of the combined treatment with 2% baking soda and ultra-sonication. In the future, the eco-friendly seed disinfection technology using ultra-sonication and baking soda is more effective and economical methods, so we need to expand research on other organic crops.