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Biofortification is the development and/or selection of micronutrient/phytonutrient rich staple crops using efficient traditional breeding techniques or modern biotechnology tools. However, even if in some cases the use of transgenic approach is crucial, consumer concerns about genetically modified organisms is increasing, which shifts most of the efforts toward the use of naturally biofortified crops. The valorization of biofortified crops is of great importance since their differences with currently and ordinary grown cultivars is clearly visible in case of high-pigment and purple tomato and colored potatoes. It has been reported that the consumption of fruit and vegetables, rich in various phytochemicals, is associated with health benefits, such as lower risk of contracting chronic diseases as well as extended shelf life and marketability compared to currently grown cultivars. In this context, the existence of genetic variability in various crops particularly, tomato (high-pigment and purple tomato) and potato (colored potato), enables the development of new crop varieties with both satisfying agronomic traits and increased functional quality. The development of such crops will contribute to satisfy the demand of (1) growers for high-income nutrient-rich crops with increased shelf life, (2) processors for high-value-added processed products with increased marketability, and (3) consumers for nutrient-rich crops and processed products as well, which will increase the intake of various phytochemicals.