Probiotics have long been used as functional starter cultures for fermented foods and are associated with numerous health benefits. We investigated the ameliorating effects of Lactiplantibacillus plantarum ZDY2013 fermented milk on disease phenotypes triggered by enterotoxigenic B. cereus in mice. Results revealed that administration of pathogenic B. cereus for one week induced damages to intestinal structures and bowel function, accompanied by an imbalance of gut microbiota, which were rescued by supplementation of L. plantarum fermented milk. Our findings revealed that L. plantarum ZDY2013 has the potential to be a fermented starter in functional foods and retains its antagonism against B. cereus pathogenesis.