Fermented camel’s milk has various health beneficial prebiotics and probiotics. This study aimed to evaluate the preventive efficacy of Bacillus amyloliquefaciens enriched camel milk (BEY) in 2-, 4- and 6-Trinitrobenzenesulfonic acid (TNBS)-induced colitis mice models. To this end, the immune modulatory effects of Bacillus amyloliquefaciens (BA) on TNF-α challenged HT29 colon cells were estimated using the cell proliferation and cytokines ELISA method. BEY was prepared using the incubation method and nutritional value was quantified by comparing it to commercial yogurt. Furthermore, TNBS-induced colitis was established and the level of disease index, pathological scores, and inflammatory markers of BEY-treated mice using macroscopic and microscopic examinations, qPCR and immunoblot were investigated. The results demonstrate that BA is non-toxic to HT29 colon cells and balanced the inflammatory cytokines. BEY reduced the colitis disease index, and improved the body weight and colon length of the TNBS-induced mice. Additionally, Myeloperoxidase (MPO) and pro-inflammatory cytokines (IL1β, IL6, IL8 and TNF-α) were attenuated by BEY treatment. Moreover, the inflammatory progress mRNA and protein markers nuclear factor kappa B (NFκB), phosphatase and tensin homolog (PTEN), proliferating cell nuclear antigen (PCNA), cyclooxygenase-2 (COX-2) and occludin were significantly down-regulated by BEY treatment. Interestingly, significant suppression of PCNA was observed in colonic tissues using the immunohistochemical examination. Treatment with BEY increased the epigenetic (microRNA217) interactions with PCNA. In conclusion, the BEY clearly alleviated the colitis symptoms and in the future could be used to formulate a probiotic-based diet for the host gut health and control the inflammatory bowel syndrome in mammals.