Controlling bioenergy-induced land-use-change emissions is key to exploiting bioenergy for climate change mitigation. However, the effect of different land-use and energy sector policies on specific bioenergy emissions has not been studied so far. Using the global integrated assessment model REMIND-MAgPIE, we derive a biofuel emission factor (EF) for different policy frameworks. We find that a uniform price on emissions from both sectors keeps biofuel emissions at 12 kg CO2 GJ−1. However, without land-use regulation, the EF increases substantially (64 kg CO2 GJ−1 over 80 years, 92 kg CO2 GJ−1 over 30 years). We also find that comprehensive coverage (>90%) of carbon-rich land areas worldwide is key to containing land-use emissions. Pricing emissions indirectly on the level of bioenergy consumption reduces total emissions by cutting bioenergy demand but fails to reduce the average EF. In the absence of comprehensive and timely land-use regulation, bioenergy thus may contribute less to climate change mitigation than assumed previously. Bioenergy has been widely viewed as an alternative for fossil fuels and an option for carbon dioxide removal, but there are doubts given the induced land-use changes. This study shows the importance of uniform regulation and comprehensive coverage of carbon-rich areas in reducing total emissions.