The emerging cellulosic-based ethanol industry will likely use corn (Zea mays L.) stover as a feedstock source. Growers wishing to maintain, or increase soil C levels for agronomic and environmental benefit will need to use C amendments such as manure, compost, or cover crops, to replace C removed with the corn stover. The objective of this research was to determine the effect of cover crops, manure, and compost on short-term C sequestration rates and net global warming potential (GWP) in a corn-soybean [Glycine max (L.) Merr.] rotation with complete corn stover removal. Field experiments consisting of a corn-soybean-corn rotation with whole-plant corn harvest, were conducted near East Lansing, MI over a 3-yr period beginning in the fall of 2001. Carbon amendments were: compost, manure, and a winter cereal rye (Secale cereale L.) cover crop. Compost and manure amendments raised soil C levels in the 0 to 5 and 0 to 25 cm soil profile but not in the 5 to 25 cm soil profile over the relatively short-term duration of the study. Total soil organic C (SOC) (kg ha-1) in the 0 to 25 cm profile increased by 41 and 25% for the compost and manure treatments, respectively, and decreased by 3% for the untreated check. Compost and manure soil amendments resulted in a net GWP of -1811 and -1060 g CO2 m-2 yr-1, respectively, compared to 12 g CO2 m-2 yr-1 for untreated.