Mucosal surfaces constitute the principal immunological interface between mammals and their environments, continuously integrating dietary antigens, the commensal microbiota, and exposure to pathogens. These barrier sites are organized into compartmentalized immune networks that coordinate epithelial surveillance, antigen sampling, immunoglobulin A (IgA) diversification, and tissue-resident immune responses. However, prevailing paradigms in mucosal immunology are derived predominantly from murine and human systems and often assume broad conservation of mucosal immune organization across mammals. Emerging comparative evidence challenges this assumption as ruminants, monogastrics, carnivores, and reservoir wildlife species exhibit substantial divergence in mucosal architecture, Peyer’s patch ontogeny, epithelial sensing pathways, and immune–microbiota interactions, reflecting adaptation to distinct ecological and dietary pressures We propose that mucosal immunity serves as an ecological filter shaping microbial persistence, pathogen shedding, and zoonotic transmission at barrier sites where pathogen emergence initiates. Failure to account for species-specific mucosal immune organization may limit cross-species extrapolation of vaccine responses, microbiome-targeted therapeutics, and zoonotic risk prediction. We further argue that variation in mucosal compartmentalization contributes directly to reservoir competence by influencing immune tolerance, microbial filtering, IgA repertoire diversification, and pathogen persistence within host populations. Finally, we identify major unresolved questions and highlight the need for comparative spatial immunology and integrated mucosal multi-omics to develop predictive models of host–pathogen interaction within a One Health framework.