Previous research from our lab showed that Bacillus siamensis, isolated from tomato seeds, significantly decreased tomato damping-off disease while also stimulating plant development. However, these bio-control agents need to be formulated to stabilize the organism, make the application easy, prolong the shelf-life, protect the organism from harsh environmental conditions, and boost the organism's activity. Therefore, we undertook the study to develop the B. siamensis-based formulation and assess its bioefficacy. For the development of liquid formulation, various chemicals such as lactose, dextrose, tween 20, and vegetable oils were evaluated. The highest survival, stability, and anti-fungal activity of B. siamensis aqueous suspension-based oil-in-water formulation was obtained with 2% soybean oil, 5% dextrose as carbon source, and 1% emulsifier along with 1% osmotic protectant in an aqueous suspension of bacterial cells. With this combination, the B. siamensis cells were able to survive up to 12 months of storage at room temperature with bacterial population of 10 7 colony forming units per milliliter (cfu/mL). The optimized liquid formulation of B. siamensis was found to significantly reduce damping-off disease by 60% when compared to only infected control. Furthermore, seed treatment boosted seed germination by 96%, as well as seedling vigor index (1580). Plant height, number of leaves, buds, flowers, and fruits increased significantly (p < 0.05) in the pot trial, with a maximum fruit yield of 1085 g/plant. In addition, when compared to the control, tomato fruits from the formulation-treated plants had higher levels of ascorbic acid (14.81 mg/100 g) and total soluble solids (TSS) (7.03 °Brix). Thus, this study provided a successful approach for the development of a liquid-based stable bioformulation of B. siamensis.