Inflammatory bowel diseases (IBDs) are characterized by dysregulated inflammatory responses, increased reactive oxygen species (ROS), and compromised intestinal barrier function. Current clinical treatments often yield suboptimal responses and significant side effects. Given the great potential of Akkermansia muciniphila (AKK) bacterial membrane components in IBD treatment and the possible pathogenicity of live bacteria, to essentially address these challenges, we develop a natural membrane-based single-cell coating, incorporating a self-assembled AKK bacterial membrane (AKM) and astaxanthin (AST), forming a protective biological barrier on probiotics. Utilizing Escherichia coli Nissle 1917 (EcN) for the oral delivery system, we engineer AKM-AST@EcN nanocoated probiotics, demonstrating exceptional gastrointestinal (GI) tract tolerance and robust bioactivity. Critically, our findings highlight the potential of AKM-AST@EcN as a promising therapeutic approach for IBD treatment while also presenting a distinctive strategy for probiotic oral delivery systems.