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.