Small-scale Jatropha cultivation and biodiesel production has the potential of contributing to local development, energy security and greenhouse gas (GHG) mitigation. In recent years however, the GHG mitigation potential of biofuel crops is heavily disputed due to the occurrence of a carbon debt, caused by CO2 emissions from biomass and soil after land use change (LUC). Most published carbon footprint studies of Jatropha report modeled results based on a very limited database. In particular, little empirical data exist on the effects of Jatropha on biomass and soil C stocks. In this study we used field data to quantify these C pools in three land uses in Mali, i.e. Jatropha plantations, annual cropland and fallow land, to estimate both the Jatropha C debt and its C sequestration potential. Four years old Jatropha plantations hold on average 2.3 Mg C ha−1 in their above- and belowground woody biomass, which is considerably lower compared to results from other regions. This can be explained by the adverse growing conditions and poor local management. No significant soil organic carbon (SOC) sequestration could be demonstrated after four years of cultivation. While the conversion of cropland to Jatropha does not entail significant C losses, the replacement of fallow land results in an average C debt of 34.7 Mg C ha−1, mainly caused by biomass removal (73%). Retaining native savannah woodland trees on the field during LUC and improved crop management focusing on SOC conservation can play an important role in reducing Jatropha's C debt. Although planting Jatropha on degraded, carbon-poor cropland results in a limited C debt, the low biomass production and seed yield attained on these lands reduce Jatropha's potential to sequester C and replace fossil fuels. Therefore, future research should mainly focus on increasing Jatropha's crop productivity in these degraded lands.This article is protected by copyright. All rights reserved.