The use of probiotic bacteria derived from fermented foods has been explored by the scientific community as alternative strategies for the treatment of several diseases, mainly regarding intestinal dysfunction. One of the most relevant inflammatory diseases affecting the alimentary tract, for which no current intervention is entirely successful, is mucositis. In this review article, we summarize the most recent proof-of-concept studies dealing with the therapeutic use of dairy origin probiotics, for the treatment of gastrointestinal mucositis. Furthermore, we discuss several approaches for the improvement of the classical therapeutic rationale, such as supplementation with prebiotics and genetic engineering along with the respective translational issues, which may be crucial for the successful transposition of these therapeutic strategies for clinical use.