Physical protection of soil organic matter by aggregates is considered to be an important mechanism for soil carbon stabilization. In this study, we evaluated the effect of drying and wetting on the interrelationships between macroaggregate formation and degradation (i.e. macroaggregate turnover), microaggregate formation within macroaggregates, and aggregate-associated carbon dynamics. Dry–wet (DW) cycles were used to simulate one of the soil aggregate disruptive effects induced by tillage. A conceptual model developed from long-term no-till (NT) and conventional tilled (CT) field experiments was then used to interpret our results. Sieved (250μm) air-dried soil samples were taken from Weld silt loam soil (Aridic Paleustoll) that had been cultivated continuously. The samples were mixed with 13C-labeled wheat and incubated for 74days. One set of soil samples was subjected to four DW cycles, while the other set was kept at field capacity (control). At days 14, 44 and 74, water-stable microaggregates (53–250μm) held within large macroaggregates (>2000μm) were isolated. Inter-and intra-microaggregate particulate organic matter (POM) fractions were separated and analyzed for total and wheat-derived C. After two DW cycles (day 44), we observed a significantly lower proportion of water-stable microaggregates within DW macroaggregates compared to control macroaggregates (9 versus 13% of the macroaggregate weight). Simultaneously, DW macroaggregates had significantly lower intra-microaggregate POM-C concentrations compared to control macroaggregates. This difference in intra-microaggregate POM-C between DW and control was more significant for native intra-microaggregate POM-C (0.73 versus 1.03gkg−1 macroaggregates) (P<0.05) than for wheat-derived intra-microaggregate POM-C (41 versus 49mg C kg−1 macroaggregates) (P<0.1). After two DW cycles (day 44), drying and wetting no longer caused macroaggregate disruption. From day 44 to day 74, both the proportion of microaggregates and the concentration of intra-microaggregate POM-C significantly increased in DW macroaggregates. We conclude that POM-C in new microaggregates within macroaggregates is inhibited by an enhanced macroaggregate turnover, which is only in the short term enhanced by drying and wetting. Furthermore, we suggest that besides a release of total (i.e. native and wheat-derived) POM upon macroaggregate breakdown, drying and wetting induced a fast reformation of macroaggregates with preferential incorporation of wheat-derived POM, resulting in a relative decline of native POM-C in DW macroaggregates.