In Asia, Pakistan’s children are more stunted and suffered from malnutrition as compared to other underdeveloped counties. Focusing the importance of wheat and malnutrition issue in Pakistan, a Field and Lab study was undertaken on 60 wheat varieties during 2017–2018 and 2018–2019 to investigate the variability and availability for trace elements such as Zn, Fe, Se, Mn, Cu under three agro-ecological locations. All three locations come under different agro-ecological conditions due to their weather, soil and morphological conditions. According to the result the tested sixty wheat varieties were ranged higher from 30.33mg kg− 1 to 51.96 mg kg− 1grain Fe, from 16.03 to 54.93 mg kg− 1grain Zn, 19.95–45.97 mg kg− 1 grain Mn, 3.16–8.98 mg kg− 1 grain Cu and 46.0-307.42µg kg− 1grains Se concentration at Hyderabad and Mirpurkhas location during both studies years as compared to Thatta location. According to the findings, out of 60 analyzed varieties, 06 showed capability to accumulate maximum concentration of for elements and among all six-supper varieties, variety IV-03 showed superiority over all by producing maximum trace element content not only at Hyderabad and Mirpurkhas but also at Thatta. By adopting such type of varieties in daily diet, Pakistan can overcome health and growth issues.