The use of the supernatant from a Bacillus subtilis culture mixed with sodium bicarbonate was explored as a means of controlling stem brown spot disease in dragon fruit plants. In in vitro experiments, the B. subtilis supernatant used with sodium bicarbonate showed a strong inhibition effect on the growth of the fungus, Neoscytalidium dimidiatum, the agent causing stem brown spot disease and was notably effective in preventing fungal invasion of dragon fruit plant. This combination not only directly suppressed the growth of N. dimidiatum, but also indirectly affected the develop- ment of the disease by eliciting the dragon-fruit plant’s defense response. Substantial levels of the pathogenesis- related proteins, chitinase and glucanase, and the phenylpropanoid biosynthetic pathway enzymes, peroxidase and phenyl alanine ammonia-lyase, were triggered. Significant lignin deposition was also detected in treated cladodes of injured dragon fruit plants in in vivo experiments. In summary, B. subtilis supernatant combined with sodium bicarbonate protected dragon fruit plant loss through stem brown spot disease during plant development in the field through pathogenic fungal inhibition and the induction of defense response mechanisms.