Food science has been increasingly linked to other fields such as medicine, veterinary science, agriculture, biology, and genetics. Metabolomics can assist those different fields by identifying connections between food quality and health, while accounting for food quality changes that result from human and environmental perturbations on the food metabolome. This chapter summarises some methods for applying metabolomics in the evaluation of food quality as it relates to genetic selection and modifications, different growing (e.g. organic vs. conventional) and rearing conditions, geographic origin, food manufacturing protocols, and the effect of digestion on the nutrient availability.