Corn (Zea mays L.) and corn stover are currently considered the most abundant and readily accessible feedstock resources for renewable bioethanol. Whole‐plant corn harvest could increase bioethanol yield compared with a conventional separated grain and stover harvest. There is limited research, however, on the environmental effects of whole‐plant harvest strategies, including nonrenewable energy efficiency, greenhouse gas (GHG) emission intensity, and soil organic C (SOC) changes. In this study, harvest methods together with bioprocessing steps were combined through life cycle analysis (LCA) models, and SOC changes for corn farming with different harvest methods were simulated by a Daycent ecosystem model. The harvest data were from four agronomy farms (Branch, Ingham, Huron, and Menominee) of Michigan State University across south to north in Michigan. The LCA results showed that a whole‐plant harvest strategy could increase energy efficiency 3.4 to 4.3 times and reduce GHG emissions by 38 ± 2% relative to a traditional separate grain and stover harvest strategy. The analyses also indicated, however, that whole‐plant harvest could reduce SOC (66.9 ± 22.9 g CO2 equivalent m−2) annually during 50 yr of continuous corn farming at Branch, Ingham, and Huron, while the conventional harvest system could sequestrate CO2 into SOC at Ingham, Huron, and Menominee. The Daycent simulation also showed that a winter cover crop planted after whole‐plant immature corn harvest could compensate for part of the SOC loss associated with a whole‐corn‐plant harvest.