Disease in food crops is a threat to food security. Previous studies have suggested that adding probiotics to soil can improve plant health and resilience. A new study examined the ecological mechanisms behind disease suppression from fertilizer amended with beneficial bacteria. To banana plants, the authors applied organic fertilizer that was either sterilized or unsterilized and either supplemented with Bacillus or not. Over 3 growth seasons, they measured the density of Fusarium wilt disease and the microbial makeup of the surrounding soil. Plants treated with Bacillus-supplemented fertilizers had reduced disease density with Bacillus supplementation more strongly suppressing disease in unsterilized fertilizer. The bacterial taxa found in the soil and the rhizosphere varied with soil treatmen. Soil supplemented with Bacillus showed an increased density of Pseudomonas, common bacteria shown to suppress disease in other studies. Bacillus supplementation may trigger a synergistic response in the soil microbiome that suppresses disease. Future work should explore the mechanisms behind the Pseduomonus and Bacillus synergy. This will aid in the development of targeted treatments to reduce disease in food crops.