In order to understand if and how composting modifies the dynamics of incorporation of organic carbon and nitrogen to soil aggregates during residue decomposition, we studied samples of a soil amended with fresh or composted plant residues in the laboratory. Samples from the surface horizon of a Luvisol (representative of large agricultural regions in northern Europe) were amended with fresh or composted 13C–15N-labelled wheat, corn and rapeseed residues and incubated in the laboratory during three years. Aggregates of samples taken at the initial time, after 45 days and after three years of incubation were fractionated by size; OC and N concentrations plus isotopic signatures of C and N were analysed in each aggregate fraction. Both fresh and composted residues addition increased aggregate stability at 45 days, but the effect almost disappeared after three years. The addition of the residues increased OC and N contents with respect to the control soils after three years. The additional OC and N coming from residues were initially incorporated preferentially into 0.05–0.2-mm aggregates, as indicated by isotopic signature analyses, and later redistributed homogeneously among all size fractions. After three years of incubation, 11% of plant residue OC remained in soil when these were added fresh, and 22% if they were previously composted, whereas similar N percentages (26–27%) remained for fresh or composted residues. Overall, a higher amount of inputs from plant residues remained in the soil in the long term when they were previously composted, with respect to non-composted residues.