Although there are many indications that N cycling in grassland ecosystems changes under elevated atmospheric CO2 partial pressure (pCO2), most information has been obtained in short-term studies. Thus, N budgets were established for four years under ambient and 60 Pa pCO2 at two levels of N fertilization in two contrasting model ecosystems: Trifolium repens L. (white clover) and Lolium perenne L. (perennial ryegrass) were planted in soil in boxes in the Swiss FACE experiment. While T. repens showed an 80% increase in harvested biomass with no change in biomass allocation under elevated atmospheric pCO2 compared to ambient conditions, L. perenne showed an increase only in the biomass of the roots. During the four years of the experiment, the systems gained N both from N retained in the soil and from stubble/stolon and roots left after the final harvest; in total between 11 and 86 gN m−2. Nitrogen retention in the soil was between 4 and 64 g m2. The L. perenne system gained the most N and retained the most N in the soil at high N fertilization and elevated atmospheric pCO2. The input of new C and N into the soil correlated well in the L. perenne systems but not in the T. repens systems. Elevated atmospheric pCO2 led neither to an increase in N retention in the soil nor did it reduce the loss of N from the soil. In the L. perenne systems, N fertilization played the main role in both the retention of N and the sequestration of C, while in the T. repens systems symbiotic N2 fixation may have controlled N retention in the soil.