Managing nitrogen (N) supply to better match crop demand and reduce losses will be an important goal under future predicted elevated carbon dioxide (e[CO2]) conditions. This study comprised two Free-Air Carbon dioxide Enrichment (FACE) experiments conducted in southern Australia in 2011. The first experiment (Exp-1) was a field experiment that investigated the impact of a nitrification inhibitor (NI), 3,4-dimethylpyrazole phosphate (DMPP), and supplementary irrigation on utilisation of legume (field pea) residual N by a wheat crop and soil nitrous oxide (N2O) emissions. The second experiment (Exp-2) used 15N techniques in soil cores to investigate the impact of DMPP on recovery of fertiliser N. In Exp-1, grain N concentration increased (by 12%, P < 0.001) with NI application compared with no NI application, irrespective of CO2 concentration ([CO2]) and supplementary irrigation. With NI application the grain N harvest index increased under e[CO2] (82%) compared with a[CO2] (79%). Applying the NI compensated for decreased grain copper concentration observed under e[CO2] conditions. NI had minimal effect on soil N2O emissions in the wheat crop regardless of [CO2]. In Exp-2, 65% (±1 standard error, n = 15) of the applied N fertiliser was recovered in the aboveground plant, irrespective of NI use. The use of a NI in a cereal–legume rotation may help to increase grain N concentration, increase the mobilisation of N towards the grain under e[CO2], and may also help to compensate for decreases in grain copper concentration under e[CO2]. However, use of a NI may not provide additional benefit for productivity or efficiency of N utilisation.