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The beneficial antimicrobial effects of high hydrostatic pressures (HHP) treatments on chill-stored seafood are well documented. Less attention has been given to their impact on the metabolic profile of the seafood, which can offer valuable insights into the preservation mechanisms of these treatments. To address this gap, the present work describes the effects of HHP on the metabolome of chill-stored grey mullet using 1H-NMR. Samples were treated with HHP at 0, 400, 500, and 600 MPa for 10 min and stored at 2–4 °C. HHP effectively inactivated Lactobacillusspp., E. coli, Pseudomonasspp., total Coliforms, and sulfite-reducing anaerobic bacteria (AB), and significantly (p < 0.05) reduced the total mesophilic bacteria (TMB). Additionally, the microbiological shelf-life of grey mullet was extended from 9 to 35 days with the application of 600 MPa HHP. Unsupervised hierarchical cluster analysis and robust Principal Component Analysis (rPCA) revealed the overall changes in metabolites’ profile caused by HHP. HHP treatment significantly reduced the formation rate of decay-related metabolites, including hypoxanthine, trimethylamine (TMA), and biogenic amines, which significantly (p < 0.05) positively correlated with all considered microorganisms. A metabolic pathway analysis revealed several pathways that may underly the spoilage of grey mullet, including tyrosine metabolism, pyruvate metabolism, lysine metabolism, glycolysis/gluconeogenesis, butanoate metabolism, citrate cycle (TCA cycle), phenylalanine metabolism, and sulfur metabolism. Interestingly, among these pathways, lysine metabolism remained unaffected by the considered HHP treatments. These findings provide a better understanding of the mechanisms underlying the effects of HHP on chilled grey mullet.