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Tritordeum is the new cereal derived from crosses between the wild barley Hordeum chilense Roem. et Schultz. and either durum or bread wheat, resulting in hexaploid and octoploid tritordeums, respectively. The success of tritordeum as a crop depends on the effectiveness of its breeding programme. In this work, new advanced tritordeum lines are screened for grain carotenoid content and disease susceptibility to analyse the impact of the current breeding strategies and to identify their strengths and putative limitations for future challenges. We conclude that selection for grain carotenoid content, the main strength for the tritordeum commercialization, should be reinforced not only by using the diversity of H. chilense but also incorporating beneficial alleles from durum wheat. Furthermore, genes for stem rust resistance from the A and B wheat genomes must be incorporated into tritordeum breeding programme. Finally, when selecting for threshability, tritordeums without chromosome substitutions should be preferentially selected using a marker‐assisted selection approach. [ABSTRACT FROM AUTHOR]