Cereals are a good source of phenolics and carotenoids with beneficial effects on human health. In this study, a 2-year evaluation was undertaken on grain, wholemeal and refined-flour of two cultivars, one old and one modern, belonging to three cereal species. Wholemeal of selected cultivars for each species was used for biscuit making. In the grain, some yield-related traits and proteins (PC) were evaluated. In the flours and biscuits, total polyphenols (TPC), flavonoids (TFC), proanthocyanidins (TPAC), carotenoids (TYPC) and antioxidant activities (DPPH and TEAC) were spectrophotometrically determined, whereas HPLC was used for the composition of soluble free and conjugated, and insoluble bound phenolic acids. Species (S), genotype (G) and ‘SxG’ were highly significant for yield-related and all antioxidant traits, whereas cropping year (Y) significantly affected yield-related traits, PC, TPC, TPAC, TEAC and ‘SxGxY’ interaction was significant for yield-related traits, TPAC, TYPC, TEAC, DPPH and all phenolic acid fractions. Apart from the TYPC that prevailed in durum wheat together with yield-related traits, barley was found to have significantly higher values for all the other parameters. Generally, the modern cultivars are richest in antioxidant compounds. The free and conjugated fractions were more representative in emmer, while the bound fraction was prevalent in barley and durum wheat. Insoluble bound phenolic acids represented 86.0% of the total, and ferulic acid was the most abundant in all species. A consistent loss of antioxidants was observed in all refined flours. The experimental biscuits were highest in phytochemicals than commercial control. Although barley biscuits were nutritionally superior, their lower consumer acceptance could limit their diffusion. New insights are required to find optimal formulations for better nutritional, sensorial and health biscuits.