Abstract. Free air CO2 enrichment (FACE) experiments in aggrading forests and plantations have demonstrated significant increases in net primary production (NPP) and C storage in forest vegetation. The extra C uptake may also be stored in forest floor litter and in forest soil. After five years of FACE treatment at the EuroFACE short rotation poplar plantation, the increase of total soil C% was larger under elevated than under ambient CO2. However, the fate of this additional C allocated belowground remains unclear. The stability of soil organic matter is controlled by the chemical structure of the organic matter and the formation of micro-aggregates (within macro-aggregates) in which organic matter is stabilized and protected. FACE and N-fertilization treatment did not affect the micro- and macro-aggregate weight, C or N fractions obtained by wet sieving. However, Populus euramericana increased the small macro-aggregate and free micro-aggregate weight and C fractions. The obtained macro-aggregates were broken up in order to isolate recently formed micro-aggregates within macro-aggregates (iM-micro-aggregates). FACE increased the iM-micro-aggregate weight and C fractions, although not significantly. This study reveals that FACE did not affect the formation of aggregates. We did, however, observe a trend of increased stabilization and protection of soil C in micro-aggregates formed within macro-aggregates under FACE. Moreover, the largest effect on aggregate formation was due to differences in species, i.e. poplar genotype. P. euramericana increased the formation of free micro-aggregates which means that more newly incorporated soil C was stabilized and protected. The choice of species in a plantation, or the effect of global change on species diversity, may therefore affect the stabilization and protection of C in soils.