We conducted a study to investigate the role of aggregates in the stabilization of residue- and root-derived C in an illitic Mollisol and a kaolinitic Oxisol under the following treatments: (i) incorporated residue, (ii) growing plants, and (iii) both incorporated residue and growing plants. Residue-C dynamics were followed in soils incubated with ¹³C-labelled wheat residue with and without unlabelled growing wheat plants. Root-C was traced by growing wheat plants with and without unlabelled wheat residue in a ¹³CO₂-labelling chamber. After 46 and 76 incubation days, residue- and root-C were measured in four aggregate size classes and in microbial-C. Both soils had greater residue-derived than root-derived total aggregate-associated C at day 76, which we attributed to the larger residue-C than root-C inputs at the start of the experiment. On an aggregate basis, the ratio of residue-derived over root-derived C decreased in most size fractions over time, indicating a greater potential for longer-term root-C than residue-C stabilization by aggregates in both soils. At both sampling days, all aggregates > 53 μm had greater residue-C concentrations in the illitic soil than in the kaolinitic soil and this difference increased with increasing aggregate size. This suggested a greater affinity of illite clay than kaolinite clay to bind with fresh residue-derived compounds into larger aggregates and hence a greater importance of aggregates in stabilizing residue-C in illitic compared with kaolinitic soils. The stabilization of root-C by aggregates was less affected by clay mineralogy and thus less dependent on the affinity of clay minerals to bind with root-derived compounds.