Correctly assessing the metabolic status of subjects after consumption of specific diets is an important challenge for modern nutrition. Recently, metabolomics has been proposed as a powerful tool for exploring the complex relationship between nutrition and health. Nutritional metabolomics, through investigating the role that dietary components play in the maintenance of health and development of risk disease, aims to identify new biomarkers that allow the intake of these compounds to be monitored and related to their expected biological effects. This review offers an overview of the application of nutrimetabolomic strategies in the discovery of new biomarkers in human nutritional research, suggesting three main categories: (1) assessment of nutritional and dietary interventions; (2) diet exposure and food consumption monitoring; and (3) health phenotype and metabolic impact of diet. For this purpose, several examples of these applications will be used to provide evidence and to discuss the advantages and drawbacks of these nutrimetabolomic strategies.