Understanding the genetic basis of micronutrient concentration in wheat grain may provide useful information to breed for biofortified varieties through marker assisted selection (MAS). One hundred and thirty eight doubled haploid progeny of a cross between the wheat cultivars ‘Berkut’ and ‘Krichauff’ were evaluated for 2 years at two locations on the eastern Gangetic plains of India under timely (November) sown conditions. Grains were evaluated for Zn and Fe concentrations by energy-dispersive X-ray fluorescence. Using composite interval mapping, three QTLs were identified; two for Zn (1B and 2B) with a QTL (2B) co-located for Fe and the third (1A), for protein. The QTL located on chromosome 1B (flanked by wmc036–cfa2129) and 2B (flanked by gwm120–wpt2430) for Zn explained up to 23.1 and 35.9 % of mean phenotypic variation respectively, whereas up to 22.2 % was explained by the Fe QTL co-located with the Zn QTL on chromosome 2B. A QTL for grain protein was detected on chromosome 1A and flanked by the markers, wpt9592 and GBM1153 which explained up to 17.7 % of the total phenotypic variation. With their detection over consecutive seasons, the detected QTLs appeared robust and useful for MAS.