Conventional tillage is a widespread soil management practice that controls weeds and promotes nutrient mineralization at the expense of a degraded soil structure and soil carbon (C) loss. Although C dynamics and soil structure are widely recognized as pivotal to essential environmental and crop-related agroecosystem processes such as belowground C storage and crop root establishment, there is still a need to evaluate cropping practices most favorable for soil structure. For example, the effects on soil structure by continuous intensive tillage after a ley period remains unclear. To address these issues, we measured mean weight diameter, total C and total nitrogen (N) in whole soil and water-stable aggregate fractions after a 4-year arable crop rotation on a Cambisol where organic and conventional management was combined with intensive tillage and different types of conservation tillage. Measurements were repeated following a 2-year grass-clover ley period. Results showed that 4 years of organic management (including the application of cattle manure slurry) combined with reduced tillage significantly improved soil structure through increasing the proportion of large macroaggregates and hence the aggregate mean weight diameter (MWD) in the 0-6 cm soil layer. Although an increase in MWD after ley was observed in organic intensive tillage and a marginal increase in conventional intensive tillage, a significant increase in total C was observed only for the organic cropping systems, which also showed a high C stratification between 0-6 cm and 6-20 cm depth. Thus, a ley period enhances soil structure after continuous cropping under intensive tillage and when organic management is combined with reduced tillage. In conclusion, soil structure is best maintained when combining organic management with reduced tillage due to additive effects.