Establishment of no-till cover crops and application of animal manure following corn (Zea mays L.) stover removal may be potential management strategies to ameliorate any negative effects that stover removal may have on soil properties and processes. We evaluated the effects of winter rye (Secale cereale L.) cover crop and beef cattle manure application on near-surface soil physical properties and soil C concentration after stover removal on an ongoing no-till continuous corn experiment established in 2010 at the University of Nebraska-Lincoln’s South Central Agricultural Laboratory near Clay Center, NE. The treatments include two levels of stover removal (0 and 85% removal), irrigation (full and deficit irrigation), and N fertilization (125 and 200 kg N ha^-1), and three organic C input treatments (cover crop, animal manure, and control). Data collected at this point, after 3 years, under full irrigation and 200 kg N ha^-1 indicate that 85% stover removal reduced the amount of water-stable aggregates, bulk density, C concentration, coarse particulate organic matter, and water retention capacity near the surface (0- to 2.5-cm depth) but had small or no effects at deeper depths. Stover harvest (85% removal) also increased wind erodible fraction and reduced geometric mean diameter of dry aggregates in the 0- to 5-cm depth under all amelioration practices (control, manure, and cover crop treatments), indicating that high rates of stover removal can increase soil’s susceptibility to wind erosion. Differences in the above properties between no stover removal and 85% stover removal with amelioration practices were not significant, which suggests that the stover-induced negative effects on these near-surface soil properties could be offset with the use of cover crops and manure. Cover crop and manure application did not, however, counteract the large increase in wind erodible and reduction in dry aggregate size with 85% stover removal.