Net benefits of bioenergy crops, including maize and perennial grasses such as switchgrass, are a function of several factors including the soil organic carbon (SOC) sequestered by these crops. Life cycle assessments (LCA) for bioenergy crops have been conducted using models in which SOC information is usually from the top 30 to 40 cm. Information on the effects of crop management practices on SOC has been limited so LCA models have largely not included any management practice effects. In the first 9 years of a long-term C sequestration study in eastern Nebraska, USA, switchgrass and maize with best management practices had average annual increases in SOC per hectare that exceed 2 Mg C year−1 (7.3 Mg CO2 year−1) for the 0 to 150 soil depth. For both switchgrass and maize, over 50 % of the increase in SOC was below the 30 cm depth. SOC sequestration by switchgrass was twofold to fourfold greater than that used in models to date which also assumed no SOC sequestration by maize. The results indicate that N fertilizer rates and harvest management regimes can affect the magnitude of SOC sequestration. The use of uniform soil C effects for bioenergy crops from sampling depths of 30 to 40 cm across agro-ecoregions for large scale LCA is questionable.