Soil aggregate dynamics have received renewed interest due to their relevance in carbon (C) stabilisation. This study evaluated changes in aggregate-size distribution and intra-aggregate C following 41 years of wheat production in semi-arid central South Africa. Management practices that have been applied for 41 years include two straw management protocols (unburned and burned), three tillage systems (no-tillage, stubble mulch and mouldboard ploughing) and two weeding methods (chemical and mechanical). Soil cores were taken at 0-10 cm and 10-20 cm depths and fractionated to aggregates of different sizes using wet sieving. All the fractions including bulk soil were analysed for C. Unburned plots had more small macro-aggregates (35% and 33%, respectively) in the 0-10 cm and 10-20 cm depths, but 26% and 27% lower large macro-aggregate and bulk C, respectively were found in the 10-20 cm depth compared to the burned plots. No-tillage stimulated re-aggregation, especially large macro-aggregates, by 68% in the 0-10 cm depth compared to stubble mulch. Small macro-aggregates, large micro-aggregates and bulk soil under no-tillage had on average 25% higher C compared to those under mouldboard ploughing in the 0-10 cm soil layer. Although signs of aggregate equilibrium state were evident, future studies focusing specifically on this subject are needed.