Nutrition provides the building blocks for growth, repair and maintenance of the body and is key to maintaining health. Exposure to fast foods, mass production of dietary components and wider importation of goods has challenged the balance between diet and health in recent decades and both scientists and clinicians struggle to characterise the relationship between this changing dietary landscape and human metabolism with its consequent impact on health.Metabolic phenotyping of foods, using high density data-generating technologies to profile the biochemical composition of foods, meals and human samples (pre and post food intake) can be used to map the complex interaction between the diet and human metabolism and also to assess food quality and safety. Here we outline some of the techniques currently used for metabolic phenotyping and describe key applications in the food sciences, ending with a broad outlook at some of the newer technologies in the field with a view to exploring their potential to address some of the critical challenges in nutritional science.