Soil acidity currently limits root growth and crop production in many regions of the world whilst increasing atmospheric CO2 concentration raises many uncertainties regarding future food supply. However, our knowledge of how elevated CO2 (eCO2) affects the performance of wheat crops grown in acid soils is limited. We investigated the effects of eCO2 on plant growth and yield of three pairs of near-isogenic hexaploid wheat lines varying in root malate and citrate efflux. These lines were grown in an acid soil under ambient CO2 (400 µmol mol-1) and eCO2 (550 µmol mol-1) in a soil free-air CO2 enrichment facility (SoilFACE). Elevated CO2 increased the total root biomass, total coarse root length and total tiller number of Al3+-tolerant lines that secrete citrate (TaMATE1B gene, citrate lines), whilst it decreased or did not change root biomass of Al3+-sensitive lines that lacked both malate and citrate efflux and Al3+-tolerant lines that only secrete malate (TaALMT1 gene, malate lines). As a result, eCO2 maintained the root-to-shoot biomass ratio of citrate lines, but decreased that of other genotypes. By contrast, eCO2 had no significant impact on total root length and total fine root length of citrate and sensitive lines, whilst it decreased those of malate lines. The grain yield increases under eCO2 were 31% of malate lines and 22% of citrate lines, whereas the sensitive lines showed a 12% reduction. Furthermore, the harvest index of malate lines tended to increase under eCO2 whereas there was no effect on other genotypes. Citrate lines also showed more frequent decreases of grain protein and mineral concentration in grains compared to malate lines. We found that eCO2 promotes coarse root growth and tiller formation in citrate lines but results in more infertile tillers, and thus limits the yield increase and potentially grain quality compared to malate lines. The reduced root elongation in malate lines under eCO2 can potentially benefit biomass allocation to grains, and thus yield. The Al3+-tolerant genes-TaALMT1 and TaMATE1B, and particularly the TaALMT1 gene, should be maintained in the hexaploid wheat germplasm for future eCO2 climates when wheat is grown in acid soils.