Cardiometabolic diseases-including Type 2 diabetes and obesity-remain leading causes of global mortality. Recent advancements in metabolomics have facilitated the identification of metabolites that are integral to the development of insulin resistance, a characteristic feature of cardiometabolic disease. Key metabolites, such as branched-chain amino acids (BCAAs), ceramides, glycine, and glutamine, have emerged as valuable biomarkers for early diagnosis, risk stratification, and potential therapeutic targets. Elevated BCAAs and ceramides are strongly associated with insulin resistance and Type 2 diabetes, whereas glycine exhibits an inverse relationship with insulin resistance, making it a promising therapeutic target. Metabolites involved in energy stress, including ketone bodies, lactate, and nicotinamide adenine dinucleotide (NAD⁺), regulate insulin sensitivity and metabolic health, with ketogenic diets and NAD⁺ precursor supplementation showing potential benefits. Additionally, the novel biomarker N-lactoyl-phenylalanine further underscores the complexity of metabolic regulation and its therapeutic potential. This review underscores the potential of metabolite-based diagnostics and precision medicine, which could enhance efforts in the prevention, diagnosis, and treatment of cardiometabolic diseases, ultimately improving patient outcomes and quality of life.