Biological evolution has produced increasing organizational complexity, from molecular systems to integrated multicellular organisms. Natural selection explains why advantageous variation persists, but sustaining increasingly complex living systems also requires mechanisms that preserve functional organization while allowing continual adaptive change. We propose that immunity is one of the principal networks providing this continuity: rather than serving solely as pathogen defense, it functions as an evolved recognition-and-regulation system that shapes compatible relationships across linked cellular, tissue, organismal, and host-associated ecological levels. Here, a compatible relationship is one that, within a defined biological context and timescale, sustains or can be regulated to restore system-level function; compatibility does not imply permanence, harmony, or the absence of conflict. Drawing on immunology, microbiology, evolutionary biology, developmental biology, and host–microbiome research, we argue that the progressive refinement of biological recognition has let increasingly complex organisms maintain functional coherence amid genetic variation, microbial interactions, developmental remodeling, and environmental change. Host defense, immune tolerance, tissue homeostasis, inflammatory regulation, and host–microbiome interactions are complementary expressions of this broader organizational function, which preserves biological integrity while accommodating innovation. Compatible biological relationships thus supply the organizational context in which complexity can accumulate, integrate new functions, and persist over evolutionary time. This is not a new mechanism of evolution, but an organizational principle unifying established findings across disciplines, positioning immunity as an important contributor to the preservation of biological organization during the continued evolution of complex life.