Reduced soil N availability under elevated CO2 may limit the plant's capacity to increase photosynthesis and thus the potential for increased soil C input. Plant productivity and soil C input should be less constrained by available soil N in an N2-fixing system. We studied the effects of Trifolium repens (an N2-fixing legume) and Lolium perenne on soil N and C sequestration in response to 9 years of elevated CO2 under FACE conditions. 15N-labeled fertilizer was applied at a rate of 140 and 560 kg N ha−1 yr−1 and the CO2 concentration was increased to 60 Pa pCO2 using 13C-depleted CO2. The total soil C content was unaffected by elevated CO2, species and rate of 15N fertilization. However, under elevated CO2, the total amount of newly sequestered soil C was significantly higher under T. repens than under L. perenne. The fraction of fertilizer-N (fN) of the total soil N pool was significantly lower under T. repens than under L. perenne. The rate of N fertilization, but not elevated CO2, had a significant effect on fN values of the total soil N pool. The fractions of newly sequestered C (fC) differed strongly among intra-aggregate soil organic matter fractions, but were unaffected by plant species and the rate of N fertilization. Under elevated CO2, the ratio of fertilizer-N per unit of new C decreased under T. repens compared with L. perenne. The L. perenne system sequestered more 15N fertilizer than T. repens: 179 vs. 101 kg N ha−1 for the low rate of N fertilization and 393 vs. 319 kg N ha−1 for the high N-fertilization rate. As the loss of fertilizer-15N contributed to the 15N-isotope dilution under T. repens, the input of fixed N into the soil could not be estimated. Although N2 fixation was an important source of N in the T. repens system, there was no significant increase in total soil C compared with a non-N2-fixing L. perenne system. This suggests that N2 fixation and the availability of N are not the main factors controlling soil C sequestration in a T. repens system.