The greenhouse gas (GHG) balance of biofuels largely hinges on the magnitude of nitrous oxide (N2O) emissions from arable soils during feedstock production, which are highly variable. Here, used an agro-ecosystem model to generate these emissions at a high resolution over the Ile-de-France region in Northern France, for a range of feedstocks. The emissions were input to a life-cycle assessment of candidate biofuel pathways: bioethanol from wheat and sugar-beet, biodiesel from oilseed rape, and ethanol from miscanthus. Compared to the widely-used methodology based on fixed emission factors, ecosystem modelling lead to 55% to 70% lower estimates for N2O emissions, emphasizing the importance of regional factors. The life-cycle GHG emissions of 1st generation biofuels were 50% to 70% lower than fossile-based equivalents, and 85% lower for cellulosic ethanol. Indirect land-use change effects negated these savings for bio-diesel and wheat ethanol, but were offset by direct effects for cellulosic ethanol.