Changes and relationships for organic C, microbial biomass C and N, and soil structural stability indices were determined at the soil surface after 10 years of direct drilling stubble retained (DDR) and stubble burnt (DDB), and cultivation with stubble burnt (CCB) for cropping systems on a sandy clay loam, duplex soil (calcic luvisol) in south-eastern Australia. Direct drilling caused a slight but significant increase in soil organic C at the 0-25 mm soil depth compared to the cultivated treatment. Microbial biomass C and N increases over the 0-100 mm soil depths were seasonal and generally greater for the DDR in comparison with DDB and CCB systems. Use of short duration wet sieving for the 0-25 mm soil depth showed a significant increase in aggregate stability for the DDR, especially for 2-10 mm sized aggregates, compared with the other tillage treatments. Such differences were reduced by standard wet sieving or use of a dispersion test illustrating the fragile nature of these unstable aggregates developed under cropping systems. Soil structural indices (water stable aggregates >2.00 mm, and >0.25 mm; mean weight diameter) were weakly correlated with increases in microbial biomass (r = 0.45, P < 0.01) and to total organic C (r = 0.35, P < 0.05). For these tillage systems, microbial biomass tended to be a poor predictor of changes in soil organic C. Overall, the long term effect of direct drilling and stubble retention in these cropping systems provided only relatively minor increases in organic C and, consequently, aggregate stability.