Abstract. Rare earth element oxides (REOs) are effective tracers to investigate soil aggregate dynamics and are also useful to quantify the interaction between C and aggregate dynamics. Although the effect of the REO labeling process on soil aggregates has been considerably investigated, its effect on soil organic carbon remains unknown. The objectives of this study were to (1) determine the effect of the labeling process on soil organic matter, (2) verify the feasibility of using REOs as tracers for investigating Andisols dry and wet sieving aggregate turnover, and (3) analyze the relationship between organic matter and aggregate dynamics during 28 days of incubation. The results showed that the soil organic carbon pool was interfered with by the labeling process, particularly with dissolved organic carbon (DOC), microbial biomass carbon (MBC), and free particulate organic matter (fPOM). Furthermore, the degree of interference was related to the soil sieving method, with the wet sieving process exerting a more significant effect on MBC and fPOM, and the dry sieving process biasing toward DOC. The close 1:1 relationship between measured aggregates and model predictions revealed that REOs are effective tracers for investigating both dry and wet sieving aggregate dynamics in Andisols. Regarding the relationship between organic matter and aggregate dynamics, dry sieving macroaggregate breakdown and restabilization were the largest, shortly appearing in the first incubation week and slowing down thereafter. This trend was also applicable for each dry sieving fraction turnover rate, which correlated significantly with fPOM (0.97, 0.99, and 0.997, P < 0.05). The turnover of wet sieving aggregates also occurred primarily in the first 7 days, but no significant relationship was observed between wet sieving aggregates and soil organic matter dynamics (P > 0.05), which was attributed to numerous wet–dry cycles during the labeling process. The results of the current study indicate that dry sieving aggregates fit better with the quantification of the relationship between aggregates and organic matter dynamics when soil organic matter dynamics were quantified using soil organic carbon pools.