Viral infections continue to pose a substantial threat to global public health and animal production systems. Increasing evidence indicates that disease outcomes are largely dictated by host immune regulation rather than viral replication alone. This review presents a comprehensive nutriomic perspective on host-directed therapeutic strategies, highlighting the role of vitamins, minerals, fatty acids, and phytochemicals in modulating systemic immune responses. We explore the mechanistic convergence of these nutrients on key immunological regulatory checkpoints, including type I interferon signaling, redox homeostasis, and immune metabolism. Particular emphasis is placed on the gut–lung axis and the contribution of microbial metabolites in strengthening mucosal resilience, a critical determinant in the context of zoonotic respiratory viral infections and livestock health. By integrating clinical evidence with molecular insights, this review emphasizes the potential of precision nutritional immunomodulation to recalibrate inflammatory thresholds and enhance vaccine-specific immune responses across species. Finally, we address key translational challenges, including nutrient bioavailability within dietary and feed matrices, and propose a systems-level framework to guide future research in nutritional immunology.