Wheat is an important cereal crop which contributes significantly in food and nutritional security of human population. Though, it contains significant quantities of protein, carbohydrate, fats, minerals, antioxidants and vitamins required for human health, there are problems with respect to the reduced bioavailability of micronutrients in human beings and monogastric animals. Therefore, production of new food crops with higher micronutrient densities along with reduced antinutritional factors, an approach often referred to as Biofortification, would lead to improved human health as well as reduced pollution and more sustainable agriculture. In this investigation, large variations have been identified in Fe (3065 ppm) and Zn (25-50 ppm) content in wheat germplasm (bread wheat) grown in India. Some progress has been obtained in understanding molecular basis of micronutrient absorption, transport and accumulation in grains using transcriptomic approach. Enhanced genetic variability in different nutritional quality traits have also been generated in high yielding backgrounds using EMS mutagenesis. 800 mutant lines in the background of PBW 502 (A leading wheat variety grown in North Western Plains Zone in India) were developed and evaluated for Fe, Zn, protein and phytase and phytic acid levels during 2014-15, 2015-16, 2016-2017 and 2017-18. Stable high yielding mutants lines having low phytic acid (0.90%) and high phytase level (>2400 FTU/kg) and high Fe (47 ppm) and Zn (45 ppm) have been developed against the value of phytic acid 1.32%, phytase 750 FTU/Kg, Fe 35 ppm and Zn 29 ppm present in PBW 502. Since, phytase levels is highly heritable trait (h2=0.96), it has been used in crossing for improving phytase levels in other high yielding backgrounds. This is the first report of evaluating large germplasm of wheat for both phytase and phytic acid levels (using microlevel tests developed in our laboratory) and also the development of high phytase and low phytic acid lines through mutation breeding. In addition, data demonstrated the use of agronomic interventions in the improvement of Fe and Zn. Progress made and future perspectives in both genetic and agronomic strategies for improvement of wheat nutritional quality will be discussed.