In this review, we focus on the mucosal immune response through Immunoglobulin A (IgA)-coated microbes and their role in gut dysbiosis in axial spondyloarthritis (axSpA) and associated inflammatory bowel disease. IgA-coated microbes contribute significantly to the microbial dysbiosis observed in axSpA, potentially driving gut inflammation and translocating outside of the gut and initiating systemic immune activation, thus contributing to disease pathogenesis. These insights will provide new avenues for understanding and treating axSpA and other immune-mediated inflammatory disorders by targeting specific host immune-microbe interactions.