To test the predictions that plants will have a larger flavonoid concentration in a future world with a CO2-enriched atmosphere, wheat (Triticum aestivum L. cv. Yecora Rojo) was grown in a field experiment using FACE (free-air CO2 enrichment) technology under two levels of atmospheric CO2 concentration: ambient (370 μmol mol−1) and enriched (550 μmol mol−1), and under two levels of irrigation: well-watered (100% replacement of potential evapotranspiration) and half-watered. We also studied the effects of CO2 on the concentration of total non-structural carbohydrates (TNC) and nitrogen (N), two parameters hypothesized to be linked to flavonoid metabolism. Throughout the growth cycle the concentration of isoorientin, the most abundant flavonoid, decreased by 62% (from an average of 12.5 mg g−1 on day of year (DOY) 41 to an average of 4.8 mg g−1 on DOY 123), whereas the concentration of tricin, another characteristic flavone, increased by two orders of magnitude (from an average of 0.007 mg g−1 of isoorientin equivalents on DOY 41 to an average of 0.6 mg g−1 of isoorientin equivalents on DOY 123). Although flavonoid concentration was dependent on growth stage, the effects of treatments on phenology did not invalidate the comparisons between treatments. CO2-enriched plants had higher flavonoid concentrations (14% more isoorientin, an average of 7.0 mg g−1 for ambient CO2 vs an average of 8.0 mg g−1 for enriched CO2), higher TNC concentrations and lower N concentrations in ukpper canopy leaves throughout the growth cycle. Well-irrigated plants had higher flavonoid concentrations (11% more isoorientin, an average of 7.1 mg g−1 for half watered vs an average of 7.9 mg g−1 for well-watered) throughout the growth cycle, whereas the effect of irrigation treatments on TNC and N was more variable. These results are in accordance with the hypotheses that higher carbon availability promoted by CO2-enrichment provides carbon that can be invested in carbon-based secondary compounds such as flavonoids. The rise in atmospheric CO2 may thus indirectly affect wheat-pest relations, alter the pathogen predisposition and improve the UV-B protection by changing flavonoid concentrations.