Improvement of grain protein content (GPC), loaf volume and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcrossing (MABC) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24 and Sr24. GPC was improved by 0.8–3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines, allowed development of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the following four cultivars: NI5439, UP2338, UP2382 and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were developed in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621 and DBW1. The improved pre-bred lines developed during the present study should prove useful for development of cultivars with improved nutritional quality associated with rust resistance in future wheat breeding programmes.