End-use quality is a crucial aspect of wheat quality, influencing the type and quality of the produced food products. It is mostly determined by the content and characteristics of the protein as well as the starch in the grain. Being a staple food, wheat provides more than 30% of the total calories and proteins in human diets globally. Wheat grain consists of a protein network, called gluten, which provides wheat doughs with their unique viscoelastic properties. The genetic improvement of end-use quality traits is indispensable to meet the requirements of grain markets, millers, and bakers. Thus, modern approaches such as proteomics and genomics are important to precisely identify alleles, genes, as well as their functions in improving end-use quality. End-use quality is mainly regulated by grain protein content, grain hardness and starch synthase genes, as well as gluten proteins, which can be exploited to improve the quality of wheat for the production of desired wheat cultivars. The aim of this review is to highlight the progress, challenges, and opportunities in breeding for end-use quality in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for end-use quality and (2) opportunities such as genomic selection, marker-assisted selection (MAS), and genetic variation in landraces and wild relatives for end-use quality improvement and the genes regulating end-use quality. Lastly, the paper discusses the prospects for future quality improvement in wheat. The review provides a comprehensive insight into the effects of genes on regulating end-use quality and serves as baseline information for wheat breeders to guide the development and deployment of wheat cultivars for future quality improvement.