In the last decade, the aquaculture sector has proven to be a key solution for supplying quality protein to populations across different social strata globally. The nutrition, health, and post-harvest sectors of the fisheries industry are important aspects to ensure food safety. Thus, the fishery industry introduced the concept of “cold chain” and “traceability,” which evolved to cater to the need for quality, safety, and affordability in the aquatic produce. At this juncture “food-omics,” a novel technique was introduced at recent times to fortify food and improve its security among consumers. This chapter introduces the application of metabolomics in ensuring aqua food security and highlights recent advancements in the field. It also encompasses the various aspects of food security with the implementation of metabolomic and its possible interventions during the pre and post-harvest processing of aqua food.