An important research target is improving the health benefits of traditional Mediterranean, durum wheat-based foods using innovative raw materials. In this study, we characterised wholemeal flours obtained from a traditional durum wheat cv. Svevo, two innovative durum wheat varieties (Svevo-High Amylose and Faridur), the naked barley cv. Chifaa and the elite lentil line 6002/ILWL118/1-1, evaluating them for targeted phytochemicals, untargeted metabolomics fingerprints and antioxidant capacity. To this aim, individual phenolic acids, flavonoids, tocochromanols and carotenoids were identified and quantified through HPLC-DAD, and the antioxidant capacities of both the extracts and whole meals were detected by ABTS assays. An untargeted metabolomics fingerprinting of the samples was conducted through NMR spectroscopy. Results showed that the innovative materials improved phytochemical profiles and antioxidant capacity compared to Svevo. In particular, Svevo-HA and Faridur had higher contents of ferulic and sinapic acids, β-tocotrienol and lutein. Moreover, Chifaa is a rich source of phenolic acids, β-tocopherols, lutein and zeaxanthin whereas lentil of flavonoids (i.e., catechin and procyanidin B2). The NMR profiles of Svevo-HA and Faridur showed a significant reduction of sugar content, malate and tryptophan compared to that of Svevo. Finally, substantial differences characterised the lentil profiles, especially for citrate, trigonelline and phenolic resonances of secondary metabolites, such as catechin-like compounds. Overall, these results support the potential of the above innovative materials to renew the health value of traditional Mediterranean durum wheat-based products.