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With the growing interest in the use of metabolomic technologies for a wide range of biological targets, food applications related to nutrition and quality are rapidly emerging. Metabolomics offers us the opportunity to gain deeper insights into, and have better control of, the fundamental biochemical basis of the things we eat. So doing will help us to design modified breeding programmes aimed at better quality produce; optimised food processing strategies and ultimately, improved (micro)nutrient bioavailability and bioefficacy. A better understanding of the pathways responsible for the biosynthesis of nutritionally relevant metabolites is key to gaining more effective control of the absence/level of presence of such components in our food. Applications of metabolomic technologies in both applied and fundamental science strategies are therefore growing rapidly in popularity. Currently, the world has two highly contrasting nutrition-related problems – over-consumption and under-nourishment. Dramatic increases in the occurrence of overweight individuals and obesity in developed countries are in staggering contrast to the still-familiar images of extreme malnutrition in many parts of the developing world. Both problems require a modified food supply, achieved through highly contrasting routes. For each, metabolomics has a future role to play and this review shall deal with this key dichotomy and illustrate where metabolomics may have a future part to play. In this short overview, attention is given to how the various technologies have already been exploited in a plant-based food context related to key issues such as biofortification, bioprotectants and the general link between food composition and human health. Research on key crops such as rice and tomato are used as illustration of potentially broader application across crop species. Although the focus is clearly on food supply, some attention is given to the complementary field of research, nutrigenomics, where similar technologies are being applied to understand nutrition better from the human side.