Black rot disease is a serious bacterial disease that harms vegetable crops of the Brassica genus (especially cabbage plants) worldwide. The causal agent, Xanthomonas campestris pv. campestris (Xcc), is a seed-borne pathogen that primarily infects seedlings. Previous studies suggest that the bacterial strain, Bacillus amyloliquefaciens PMB05, can intensify the plant immune responses of cabbage against black rot disease and reduce disease occurrence. In plant immunity, several reactions occur during a pathogen attack, but the elevation of calcium ion concentration in plant cells is essential in the induction of plant defense responses. Therefore, this study aims to investigate whether disease control of black rot disease in cabbage plants can be improved by integrating calcium carbonate in the formulation for preparing B. amyloliquefaciens PMB05. Firstly, we found the addition of calcium carbonate in the formulation revealed to have significantly increased the cell and endospore populations of B. amyloliquefaciens PMB05 in the fermentation liquids. To increase the convenience of disease control in the field, these fermentation liquids were converted to powder form for subsequent analysis. Results revealed that the grown seedlings from seeds, mixed with PMB05 powders, significantly intensified plant immune responses and improved black rot disease control. We further compared distinct seed treatments using one PMB05 powder to evaluate its feasibility in field application. The results demonstrated that the disease control efficacy and yield of cabbage were significantly improved in the seed treatment with the powder (SD-160C2) to 56.46% and 5.91%, respectively, at 10 weeks post transplanting. Interestingly, the seed treatment combined with a calcium-containing commercial fertilizer spraying treatment did not increase the control efficacy of black rot disease, but it significantly increased the weight of cabbages after harvest. We concluded that the seed treatment with calcium carbonate-containing Bacillus amyloliquefaciens PMB05 powder is an efficient way to control black rot disease in cabbage.