Crop residues are a potential source for biofuel production. Yet, impacts of removal of corn (Zea mays L.) stover and other residues as biofuel feedstocks on micro-scale soil properties affecting the behavior of the whole soil are not well understood. Data on both macro- and micro-scale soil properties under different scenarios of stover management are needed to define the threshold levels of stover removal. Previous studies on stover removal impacts on soil properties have primarily focused on macroscale properties and little or not on microscale properties. Thus, this study was designed to assess impacts of annual stover removal for 3 consecutive years at rates of 0, 25, 50, 75, and 100% on soil physical properties at the aggregate level under no-tillage (NT) continuous corn systems in a Rayne silt loam (RSL) (fine-loamy, mixed, active, mesic Typic Hapludult) with 10% slope, Celina silt loam (CSL) (fine, mixed, active, mesic Aquic Hapludalfs) with 2% slope, and Hoytville clay loam (HCL) (fine, illitic, mesic Mollic Epiaqualfs) with < 1% slope in Ohio. Aggregates were sensitive to stover removal particularly in the 0- to 10-cm soil depth. Stover removal reduced aggregate stability, tensile strength (TS), water retention (WR), and subcritical water repellency, while it increased water sorptivity but had no effect on pore-size distribution within an aggregate. The interaction of aggregate stability, strength, and subcritical water repellency with aggregate structural properties due to stover removal depended on the variable antecedent soil water conditions. The aggregate stability and strength decreased while water repellency increased with increasing water potential. Impacts of stover removal on the clayey soils were equal to or higher than those on silt loam soils. Removal at rates ? 25% reduced the raindrop kinetic energy (KE) required to break aggregates by 13 times at HCL, while removal at rates ? 50% reduced the KE by 2 to 3 times at RSL and CSL for air-dry aggregates. The KE and TS decreased with increasing soil water potentials. The TS was reduced by 10% to 30% at all water potentials at RSL, by 20% to 35% between - 0.1 and - 1.5 MPa, and by 2.2 times at - 166 MPa at CSL, and by 2 to 3 times between - 1.5 and - 166 MPa at HCL under complete stover removal. Removal of stover at rates ? 50% reduced subcritical water repellency by 2 to 10 times in all soils. Overall, stover removal altered micro-scale soil properties, and complete stover removal had the most detrimental effects. Based on the data from previous studies on macroscale soil properties and this study, stover removal adversely affects both macro- and micro-scale soil properties.