Metabolomics is one of the most reliable and widely used approaches to reveal the identity of a variety of bioactive metabolites. It is referred to as ‘Foodomics’ in food science and as ‘Nutrimetabolomics’ in nutrition. Nutrimetabolomics has been effectively used in nutritional sciences for intervention studies, identification of dietary biomarkers, and to study the role of metabolomics phenotyping in personalized nutrition for diet-related disorders, such as type 2 diabetes, obesity, metabolic syndrome, and prediabetes. NMR-based nutrimetabolomics has been preferred over the other approaches due to its reliability, sensitivity, reproducibility, and specificity in detecting metabolites relating to human nutrition and metabolic disorders. Clinical samples such as blood, urine, and feces could be analyzed for specific biomarkers involving NMR spectroscopic investigation followed by chemometric analysis. In this review, we have focused on NMR-based nutrimetabolomics strategies and their role in identifying dietary and disease related biomarkers of significance to human nutrition and health. Moreover, this NMR-based metabolomics can play a significant role in determining, understanding, and regulating metabolites involved in the multidimensional and complex area of functional foods and diet-related metabolic diseases. This will disclose the application of NMR nutrimetabolomics in advanced precision and personalized nutrition, food authentication, and diet-oriented disease management system.