It is now well documented that the diet has a significant impact on human health and well-being. However, the complete set of small molecule metabolites present in foods that make up the human diet and the role of food production systems in altering this food metabolome are still largely unknown. Metabolomic platforms that rely on nuclear magnetic resonance (NMR) and mass spectrometry (MS) analytical technologies are being employed to study the impact of agricultural practices, processing, and storage on the global chemical composition of food; to identify novel bioactive compounds; and for authentication and region-of-origin classifications. This review provides an overview of the current terminology, analytical methods, and compounds associated with metabolomic studies, and provides insight into the application of metabolomics to generate new knowledge that enables us to produce, preserve, and distribute high-quality foods for health promotion.