Elevated [CO2] is suggested to mitigate the negative effects of water stress in plants; however responses vary among species. Fructans are recognised as protective compounds against drought and other stresses, as well as having a role as reserve carbohydrates. We analysed the combined effects of elevated [CO2] and water deficit on fructan metabolism in the Cerrado species Viguiera discolor Baker. Plants were cultivated for 18 days in open-top chambers (OTC) under ambient (∼380 ppm), and high (∼760 ppm) [CO2]. In each OTC, plants were submitted to three treatments: (i) daily watering (control), (ii) withholding water (WS) for 18 days and (iii) re-watering (RW) on day 11. Analyses were performed at time 0 and days 5, 8, 11, 15 and 18. High [CO2] increased photosynthesis in control plants and increased water use efficiency in WS plants. The decline in soil water content was more distinct in WS 760 (WS under 760 ppm), although the leaf and tuberous root water status was similar to WS 380 plants (WS under 380 ppm). Regarding fructan active enzymes, 1-SST activity decreased in WS plants in both CO2 concentrations, a result consistent with the decline in photosynthesis and, consequently, in substrate availability. Under WS and both [CO2] treatments, 1-FFT and 1-FEH seemed to act in combination to generate osmotically active compounds and thus overcome water deficit. The proportion of hexoses to sucrose, 1-kestose and nystose (SKN) was higher in WS plants. In WS 760, this increase was higher than in WS 380, and was not accompanied by decreases in SKN at the beginning of the treatment, as observed in WS 380 plants. These results suggest that the higher [CO2] in the atmosphere contributed to maintain, for a longer period, the pool of hexoses and of low DP fructans, favouring the maintenance of the water status and plant survival under drought.