Corn stover (CS) contains high moisture in the fall and farmers keep it unharvested until next spring for its natural drying. CS contains 70% more carbon than other grain crop residues. Farmers traditionally use a portion of CS for livestock bedding and cattle feed but the rest is kept unharvested. Potential soil erosion, carbon sequestration, and nutrient removal concerns might be considered before CS harvesting. Hydrothermal carbonization (HTC) of wet biomass can produce energy dense solid bio-carbon. Hydrothermal process water (HTPW) can produce energy and recover nutrient in anaerobic digestion (AD). This study reported the results of various experiments performed on non-rooted fall harvested CS of an Ontario farm. Ontario CS was finally assessed for techno-economic and environmental aspects. This research showed 78% energy and a portion on nutrients as liquid bio-fertilizer of fall harvested CS are recoverable. Corn roots with 6–10 cm stalks, cobs and husks can be kept in the soil to recover soil organic matter (SOM) and protection of soil erosion. The process indicates the sustainable CS harvesting in the fall with possibility to reduce 75% of existing harvesting cost and reduction of greenhouse gas (GHG) emission.