Micronutrient malnutrition, characterised by vitamins and mineral deficiency, affects almost 2 billion people across all age-groups and genders and is endemic to both developing and developed countries. Besides causing specific deficiencies, it also aggravates other infectious and chronic diseases, resulting in almost 80% deaths in developing regions. Identifying health benefitting characteristics and micronutritional richness in traditional crops, and breeding them into staple crops consumed on daily basis, offers a low cost sustainable food-based solution to the problem. A traditional crop grown in most marginal areas of Africa and Asia, finger millet, is a rich source of health benefitting micronutrients, phytochemicals, vitamins and several essential amino acids. To better understand genetic control of these health benefitting traits and to breed them effectively into other staple crops, we are making use of genetics and genomics approaches. We have assembled a set of 190 genotypes incorporating a minicore collection of finger millet together with a number of elite breeding lines to capture and characterise entire genetic variation associated with such traits in finger millet gene bank. These genotypes have been extensively characterised for micronutrients (such as iron, zinc, calcium, magnesium, sodium, and potassium), protein and anti-nutrients (phytate and oxalate). Further, large-scale genotype-by-sequencing performed on these genotypes has generated 156,157 SNPs across these germplasms and breeding lines. Genome-wide association analysis of these data has identified a number of genomic regions associated with both the health benefitting traits as well as with other factors that affect their bioavailability. These findings are also paving ways of assessing how such genetic variations are distributed in other staple crops. Progress made in the project so far and of our future directions will be discussed.