There are several factors, such as nutrition, environmental factors, and exposure to toxins, that have a major influence on the risk of many diseases, including hypertension, diabetes, and overall health. The analysis of small molecules contained in biological materials is referred to as metabolomics. In recent times, the use of metabolomics in nutritional science has grown, with new research promoting a variety of applications. Discovering new genetic variants to identify metabolic disorders as quickly as possible and anticipating personal health improvements to strengthen dietary guidelines for specific ethnic groups is a major challenge nowadays. Even though only a few genetic markers have been confirmed so far, omics techniques involving genome, transcription, proteomes, and metabolites, together with computational and biostatistical, approaches have already shown considerable promise in this field of research. Over the last 20 years, major innovations have been used to classify as many substances as possible in human biofluids, such as saliva, blood, and urine. In the context of food science, several surveys on food authenticity, consistency, security, and safety, as well as food manufacturing, have been conducted. Furthermore, a metabolomic study has been conducted in order to discover new early biochemical impairment risk factors and predictive biomarkers for the development of afflictions. The use of metabolomics in identifying or developing objective biomarkers of dietary intake, developing personalized nutrition strategies, and conducting large-scale epidemiology studies to understand the connection between diet and health are just a few examples. The development of research methods for predicting and evaluating nutrient intake is also prioritized. Metabolomics is successfully developed for nutrition research; it has the ability to improve dietary assessment, assist in the delivery of personalized nutrition, and develop our awareness of the relation between diet and health and how it changes from equilibrium to disturbance.