Previous studies have shown that elevated levels of carbon dioxide [CO2] may increase, decrease, or have no effect on the concentrations of phenolic compounds in plants. The underlying causes of these variations in responses remain poorly understood. In the present study, it was hypothesized that different plant responses come mainly from the duration of exposure to the gas, growing conditions, and sampling procedures. A two-year field study was conducted in open-top chambers (375 vs. 550 μmol CO2 mol−1 air) using a japonica rice variety (Oryza sativa L. cv. Ariete) as the test crop, with plants grown under elevated [CO2] during their entire life cycle. Leaf, stem and root samples were collected at five different growth stages, and submitted to a series of physiological and biochemical measurements. The carbon:nitrogen ratio and total non-structural carbohydrates were increased by elevated [CO2] in all plant tissues. Data showed that under elevated [CO2], there was a reduction in the total phenolic and total flavonoid contents measured during the seedling, tillering, elongation, and flowering stages in all plant organs, probably resulting from a relaxation of the antioxidative system during seed germination. By contrast, the total phenolic and flavonoid contents increased under elevated [CO2] at maturity, a change in response which coincided with acclimation of photosynthesis. The same trends were observed for sixteen individual phenolic compounds, including the allelopathic tricin, the phytoalexin sakuranetin and several O-glycosylated flavonoids of ecological importance. Overall, the results indicated that during the early stages of plant development, photosynthates were mainly used to synthesize proteins and meet the growth demand of the plant. Growth reduction at maturity made more resources available for the synthesis of phenolic compounds.