About half of the world population suffers from the malnutrition of iron, zinc, calcium, iodine and selenium. Most of the major staple crops of the world, such as rice, wheat, cassava, beans, sweet potato, pearl millet or maize are often deficient in some of these mineral elements. Hence, increasing the concentration of bioavailable micronutrients in edible crop tissues (biofortification) has become a promising strategy in modern agriculture, allowing the access of more nutritious foods, to more people, with the use of fewer resources. Traditional agricultural practices can partly enhance the nutritional value of plant foods, but the advances in the 'omics' technologies are rapidly being exploited to engineer crops with enhanced key nutrients. Ionomics, or the study of the ionome (which can be defined as the mineral trace element composition of a particular organism), is a modern functional genomics tool that can provide high throughput information about the broad spectrum nutrient composition of a given plant food. In alliance with other 'omics' technologies, such as genomics, transcriptomics and proteomics it can be used to identify numerous genes with important roles in the uptake, transport and accumulation of mineral nutrients in plant foods, in particular in their edible parts. This review provides a critical comparison of the strategies that have been developed to diminish nutrient deficiencies in plant-based foods (SWOT analysis) and a summary of the gene families involved in the mineral nutrient pathways. Finally, it also discusses how 'omics' techniques can be used in genetic engineering programs to increase mineral levels and bioavailability in the most important staple food crops and the socioeconomic implications of plant-based biofortified foods.