The International Atomic Energy Agency (IAEA) Technical Cooperation Project TUN5032, also known as AquaVac-ir (http://www.aquavac-ir.tn/), seeks to establish Tunisia’s first national certified pipeline for the production of aquaculture vaccines using irradiation technology. This ambitious initiative integrates five distinct processes, each contributing innovative approaches to advance the field of aquaculture vaccine development and application. In Process 1, comprehensive immune response assessment is achieved by integrating proteomics, transcriptomics, and flow cytometry techniques. This novel approach offers a holistic view of the immune response in Dicentrarchus labrax (European seabass) following vaccination with irradiated nodavirus. Process 2 focuses on utilizing radiation-inducible promoters and expanded bacterial periplasms in selected radioresistant strains to produce nodavirus capsid proteins. In Process 3, strategies are developed to preserve epitopes of lethally irradiated nodavirus, including the use of native in silico-predicted radioprotective decapeptides from Deinococcus radiodurans. Process 4 applies artificial intelligence (AI) algorithms to predict the immunogenicity and reactogenicity signatures of irradiated vaccines, enhancing the efficacy and safety of vaccine development. Finally, Process 5 employs systems biology to construct a metabolic interaction model between European seabass and nodavirus, providing a deeper understanding of host-pathogen dynamics. Through these five innovative processes, the AquaVac-ir project aims to revolutionize aquaculture vaccine development, setting a new standard for the creation of highly effective and precisely engineered vaccines. This project represents a significant leap forward in aquatic health and vaccine production technologies.