The contribution of biofuels to the saving of greenhouse gas (GHG) emissions has recently been questioned because of emissions resulting from land use change (LUC) for bioenergy feedstock production. We investigate how the inclusion of the carbon effect of LUC into the carbon accounting framework, as scheduled by the European Commission, impacts on land use choices for an expanding biofuel feedstock production. We first illustrate the change in the carbon balances of various biofuels, using methodology and data from the IPCC Guidelines for National Greenhouse Gas Inventories. It becomes apparent that the conversion of natural land, apart from grassy savannahs, impedes meeting the EU’s 35% minimum emissions reduction target for biofuels. We show that the current accounting method mainly promotes biofuel feedstock production on former cropland, thus increasing the competition between food and fuel production on the currently available cropland area. We further discuss whether it is profitable to use degraded land for commercial bioenergy production as requested by the European Commission to avoid undesirable LUC and conclude that the current regulation provides little incentive to use such land. The exclusive consideration of LUC for bioenergy production minimizes direct LUC at the expense of increasing indirect LUC.