In modern science and technology, it is often underappreciated that foods from a chemical, physical and biological perspective are complex multifactorial systems that are extremely difficult to measure and evaluate. From a chemical perspective, foods are complex chemical mixtures of heterogeneous classes of molecules dominated by the four basic food constituents: water, fats, carbohydrates and proteins. To add further complexity, food manufacturing processes often consists of a series of unit operations that are designed to induce certain functional traits to the food materials being processed. This chapter will seek to give an overview of the possibilities and limitations of using the 1H NMR metabolomics platform to study food and food systems (foodomics). The merger of food science with advanced analytical tools, such as high-resolution NMR and multivariate data analysis chemometrics, has proven to be tremendously successful. The “weak whispers” from the protons in our food have been proven to contain a plethora of information about our aliments and to be useful in multiple applications within advanced quality control, which is not possible with existing optical spectroscopies, in particular for addressing the multiple and systemic issues related to safety and quality of food.