This review paper analyzes recent advancements in bio-polymer coatings for probiotic microencapsulation, with a particular emphasis on chitosan and its synergistic combinations with other materials. Probiotic microencapsulation is essential for protecting probiotics from environmental stresses, enhancing their stability, and ensuring effective delivery to the gut. The review begins with an overview of probiotic microencapsulation, highlighting its significance in safeguarding probiotics through processing, storage, and gastrointestinal transit. Advances in chitosan-based encapsulation are explored, including the integration of chitosan with other bio-polymers such as alginate, gelatin, and pectin, as well as the application of nanotechnology and innovative encapsulation techniques like spray drying and layer-by-layer assembly. Detailed mechanistic insights are integrated, illustrating how chitosan influences gut microbiota by promoting beneficial bacteria and suppressing pathogens, thus enhancing its role as a prebiotic or synbiotic. Furthermore, the review delves into chitosan's immunomodulatory effects, particularly in the context of inflammatory bowel disease (IBD) and autoimmune diseases, describing the immune signaling pathways influenced by chitosan and linking gut microbiota changes to improvements in systemic immunity. Recent clinical trials and human studies assessing the efficacy of chitosan-coated probiotics are presented, alongside a discussion of practical applications and a comparison of in vitro and in vivo findings to highlight real-world relevance. The sustainability of chitosan sources and their environmental impact are addressed, along with the novel concept of chitosan's role in the gut-brain axis. Finally, the review emphasizes future research needs, including the development of personalized probiotic therapies and the exploration of novel bio-polymers and encapsulation techniques.