Metabolic disorders (MDs) are characterized by disruptions in normal metabolic processes, often leading to impaired carbohydrate, lipid, or protein metabolism. These disorders, including diabetes mellitus, phenylketonuria, and lysosomal storage diseases, occur due to genetic mutations, environmental influences, or their interplay. In recent decades, nutrigenomics (NG) has arisen as a promising field, in which nutrition plays a key role in understanding the interactions between nutrients and gene expressions. By elucidating the molecular mechanisms linking dietary components to metabolic pathways, NG enables the development of personalized nutrition strategies that could prevent or alleviate MDs. For instance, individuals with type 2 diabetes may benefit from dietary modifications targeting genes that are involved in insulin signaling pathways, while those with phenylketonuria require tailored diets that are low in phenylalanine. Advances in NG technologies, such as transcriptomics and epigenomics, have revealed how nutrients influence gene expression through different mechanisms, including DNA methylation and histone modification. These findings underscore the importance of dietary patterns in mitigating the risk of MDs and improving disease outcomes. Furthermore, NG contributes to precision medicine by identifying genetic polymorphisms that affect nutrient metabolism and enabling interventions that are aligned with an individual's genetic profile. As research progresses, the integration of NG into clinical practice holds potential to revolutionize the prevention and management of metabolic disorders, promoting improved health outcomes. This systematic review aims to compile and analyze the current evidence on the role of NG in the prevention of MDs, focusing on its potential application in precision and preventive medicine. By synthesizing recent findings, this review highlights opportunities and limitations for integrating NG insights into clinical practice, helping lay the groundwork for innovative strategies to mitigate the global burden of metabolic disorders.