Conservation agriculture (CA) is regarded by many as a sustainable intensification strategy. Minimal soil disturbance in combination with residue retention are important CA components. This study examined the long-term effects of crop rotation, residue retention, and tillage on soil pore characteristics of two Danish sandy loams. Rotation R2 is a rotation of winter crops (mainly cereals) with residues retained, rotation R3 a mix of winter and spring crops (mainly cereals) with residues removed, and rotation R4 the same mix of winter and spring crops, but with residues retained. Each rotation included the tillage treatments: moldboard plowing to 20-cm depth (MP), harrowing to 8- to 10-cm depth (H) and direct drilling (D). Soil cores were taken from the topsoil (4–8, 12–16, 18–27 cm) in mid-autumn 2013 and early spring 2014. Water retention, air permeability, and gas diffusivity was determined for the first two depths (100-cm3 cores), and air permeability for the 18- to 27-cm depth (250-cm3 cores). Moldboard plowing resulted in the best soil quality at two upper depths with higher total porosity, air-filled porosity, air permeability, and gas diffusivity compared with reduced tillage. For instance, the volume of pores > 30 µm was more than 0.03 m3 m-3 larger for MP than for D in spring 2014 at the 4- to 8-cm depth. At the 18- to 27-cm depth, direct drilling resulted in a better air permeability and pore continuity index (e.g., air permeability of 18.2 and 11.2 μm2 for D and MP, respectively at −10 kPa for the Foulum location). Residue retention, especially when combined with direct drilling, increased total porosity, air-filled porosity, air permeability, and gas diffusivity and decreased blocked air porosities. Our results suggest residue management can be used to alleviate the negative effects of reduced tillage on soil structural quality.