Seafood is a valuable component of human diet because of its nutritional properties. The Atlantic bluefin tuna Thunnus thynnus is a scombroid fish highly appreciated as seafood worldwide. Being a top pelagic predator, concerns have been raised over human health risks due to its consumption. Therefore, herein it was comprehensively evaluated the health status and potential metabolite shifts between sexes of bluefin tuna from the Mediterranean Sea, proved to bioaccumulate environmental obesogens, namely polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) at hepatic level. To this aim, nuclear magnetic resonance (NMR)-based metabolomics was applied on liver of post-spawning tuna. Findings from this study pointed out that hepatic bioaccumulation of PCBs and OCPs induced differential metabolic disturbances between sexes, attributable to the reproductive stage at which tuna were caught. Alterations were mainly found in energy-producing metabolic pathways (with changes in acetate, acetoacetate, malonate, and lactate), amino acid (with changes in BCAA, alanine, sarcosine, and tyrosine), and lipid (with changes in choline and phosphocholine) metabolism, with activation of fatty acids biosynthesis and ketogenesis in male tuna. Overall, according to the current European legislation on maximum levels of contaminants in seafood, the consumption of bluefin tuna does not represent a risk for human health.