The influence of N availability on C sequestration under prolonged elevated CO2 in terrestrial ecosystems remains unclear. We studied the relationships between C and N dynamics in a pasture seeded to Lolium perenne after 8 years of elevated atmospheric CO2 concentration (FACE) conditions. Fertilizer-15N was applied at a rate of 140 and 560 kg N ha2−1 y2−1 and depleted 13C-CO2 was used to increase the CO2 concentration to 60 Pa pCO2. The 13C–15N dual isotopic tracer enabled us to study the dynamics of newly sequestered C and N in the soil by aggregate size and fractions of particulate organic matter (POM), made up by intra-aggregate POM (iPOM) and free light fraction (LF). Eight years of elevated CO2 did not increase total C content in any of the aggregate classes or POM fractions at both rates of N application. The fraction of new C in the POM fractions also remained largely unaffected by N fertilization. Changes in the fractions of new C and new N (fertilizer-N) under elevated CO2 were more pronounced between POM classes than between aggregate size classes. Hence, changes in the dynamics of soil C and N cycling are easier to detect in the POM fractions than in the whole aggregates. Within N treatments, fractions of new C and N in POM classes were highly correlated with more new C and N in large POM fractions and less in the smaller POM fractions. Isotopic data show that the microaggregates were derived from the macro-aggregates and that the C and N associated with the microaggregates turned over slower than the C and N associated with the macroaggregates. There was also isotopic evidence that N immobilized by soil microorganisms was an important source of N in the iPOM fractions. Under low N availability, 3.04 units of new C per unit of fertilizer N were sequestered in the POM fractions. Under high N availability, the ratio of new C sequestered per unit of fertilizer N was reduced to 1.47. Elevated and ambient CO2 concentrations lead to similar 15N enrichments in the iPOM fractions under both low and high N additions, clearly showing that the SOM-N dynamics were unaffected by prolonged elevated CO2 concentrations.