Due to the high environmental risks of fungicides, biological control of plant diseases with bio-factor are highly encouraged and recommended as well as trying to use natural products such as oils and plant extracts as alternatives to fungicides. Greenhouse and field experiments were conducted in 2017/2018 and 2018/2019 to study the effect of Bacillus subtilis, when applied as soil treatment in combination with different concentrations of essential plant oils as dipping treatment on onion pink rot disease. Oils of cumin, cardamom and thyme were tested at five concentrations (0.25%, 0.50%, 1%, 2%, and 4%), on the linear growth of Setophoma (Pyrenochaeta) terrestris isolates. Thyme oil had the strongest inhibitory effect on linear growth followed by cumin oil. Moreover, the reduction of linear growth increased by increasing concentration of the tested essential plant oils. Under artificial and natural infection conditions in greenhouse and field trials, when applying B. subtilis with essential plant oils at different concentrations led to significantly effect in reducing incidence of onion pink root rot, compared with untreated control. Also, all tested treatments increased fresh and dry weight under greenhouse conditions as well as increased onion bulb yield in field trials. Data also clearly showed that, there is a positive significant relationship between increase of plant oils concentrations and increase their effect on the incidence of onion pink root rot. Generally, thyme oil at 4% with B. subtilis followed by cumin at 4% with B. subtilis gave the highest percentage of healthy plants as well as the highest efficacy in reducing onion pink root rot compared to other treatments. These results suggest that, one of the means to achieve the goal of sustainable agriculture in controlling of onion pink root rot disease alongside improving onion productivity can be achievement by using of these environmentally safe treatments.