Conventional intensive 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. Alternative soil management practices such as no tillage, reduced tillage and temporary leys, however, can minimize the negative effects of intensive tillage on soil structure. To improve understanding of these management practices on soil structure, we sampled a field trial combining organic and conventional crop management with different intensity levels of tillage, resulting in four cropping systems: conventional intensive tillage (C-IT), conventional no tillage (C-NT), organic intensive tillage (O-IT) and organic reduced tillage (O-RT). A ley period was added following a 4-year arable crop rotation. We measured mean weight diameter (MWD), total C and total nitrogen (N) in whole unfractionated soil and water-stable aggregate fractions after the 4-year arable crop rotation and again after a following 2-year grass-clover ley period, to assess the impact of the cropping system and the ley, respectively. Results showed that 4 years of organic crop management including the application of cattle manure slurry combined with reduced tillage led to significantly better soil structure (i.e. aggregate MWD) at the 0–6 cm soil depth, compared to the other cropping systems tested. After the ley period, the proportion of large macroaggregates increased by 65% for C-IT and 47% for O-IT at 0–6 cm depth. Total C increased significantly for only O-IT and O-RT after the ley, both of which also showed a high C stratification between 0–6 cm and 6-20 cm depth. In conclusion, soil structure is most improved during continuous cropping when combining organic crop management with reduced tillage, while a ley period was effective in improving the soil structure in intensive tillage plots to the level of O-RT.