Monitoring soil health indicators (SHI) will help ensure that corn (Zea mays L.) stover harvest is sustainable. This study examines SHI changes after 5 yr of growing continuous corn with either chisel plow or no-tillage practices and harvesting 0, ∼35, or ∼60% of the stover. Two no-tillage treatments with a cereal rye (Secale cereale L.) cover crop and stover harvest rates of ∼35 or ∼60% were evaluated. All eight treatments were replicated four times in a randomized complete block design at an 11-ha site in Boone County, IA. Soil samples were collected following grain and stover harvest from 0- to 5- and 5- to 15-cm depth increments. Particulate organic matter C (POM-C) decreased when stover was removed or the soil was chisel plowed. No-till with 0% stover removal had 10 mg g–1 POM-C in the 0- to 5-cm soil layer, which was 1.9-fold higher than in other treatments. Potentially mineralizable N (PMN) was greater under cover crop treatments. Average PMN values were 56.9 and 45.5 µg g–1 PMN for no-till with cereal rye at 0- to 5- and 5- to 15-cm depths, respectively, compared with 17.5 and -3.7 µg g–1 PMN for the same no-till treatments without cereal rye. Other soil properties did not respond to increasing levels of stover removal. At this location and at the studied removal rates, 5 yr of harvesting corn stover did not decrease soil health, but POM-C data suggest that changes may be occurring. Long-term monitoring should continue to assess corn stover harvest sustainability.