One potentially significant impact of growing biofuel crops will be the sequestration or release of carbon (C) in soil. Soil organic carbon (SOC) represents an important C sink in the lifecycle C balances of biofuels and strongly influences soil quality. We assembled and analyzed published estimates of SOC change following conversion of natural or agricultural land to biofuel crops of corn with residue harvest, sugarcane, Miscanthus x giganteus, switchgrass, or restored prairie. We estimated SOC losses associated with land conversion and rates of change in SOC over time by regressing net change in SOC relative to a control against age since establishment year. Conversion of uncultivated land to biofuel agriculture resulted in significant SOC losses – an effect that was most pronounced when native land was converted to sugarcane agriculture. Corn residue harvest (at 25–100% removal) consistently resulted in SOC losses averaging 3–8 Mg ha⁻¹ in the top 30 cm, whereas SOC accumulated under all four perennial grasses, with SOC accumulation rates averaging <1 Mg ha⁻¹ yr⁻¹ in the top 30 cm. More intensive harvests led to decreased C gains or increased C losses – an effect that was particularly clear for residue harvest in corn. Direct or indirect conversion of previously uncultivated land for biofuel agriculture will result in SOC losses that counteract the benefits of fossil fuel displacement. Additionally, SOC losses under corn residue harvest imply that its potential to offset C emissions may be overestimated, whereas SOC sequestration under perennial grasses represents an additional benefit that has rarely been accounted for in life cycle analyses of biofuels.

In the US, 95% of biofuel is produced from corn (Zea mays L), an intensively managed annual crop that is also grown for food and animal feed. Using the DAYCENT model, we estimated the effects on ecosystem services of replacing corn ethanol feedstocks with the perennial cellulosic feedstocks switchgrass (Panicum virgatum L) and miscanthus (Miscanthus × giganteus Greef et Deuter). If cellulosic feedstocks were planted on cropland that is currently used for ethanol production in the US, more ethanol (+82%) and grain for food (+4%) could be produced while at the same time reducing nitrogen leaching (−15 to −22%) and greenhouse‐gas (GHG) emissions (−29 to −473%). The GHG reduction was large even after accounting for emissions associated with indirect land‐use change. Conversion from a high‐input annual crop to a low‐input perennial crop for biofuel production can thus transition the central US from a net source to a net sink for GHGs.