We present an approach for providing quantitative insight into the production-ecological sustainability of biofuel feedstock production systems. The approach is based on a simple crop-soil model and was used for assessing feedstock from current and improved production systems of cassava for bioethanol. Assessments were performed for a study area in Mozambique, a country considered promising for biomass production. Our focus is on the potential role of smallholders in the production of feedstock for biofuels. We take cassava as the crop for this purpose and compare it with feedstock production on plantations using sugarcane, sweet sorghum and cassava as benchmarks. Production-ecological sustainability was defined by seven indicators related to resource-use efficiency, soil quality, net energy production and greenhouse gas (GHG) emissions. Results indicate that of the assessed systems, sugarcane performed better than cassava, although it requires substantial water for irrigation. Targeted use of nutrient inputs improved sustainability of smallholder cassava. Cassava production systems on more fertile soils were more sustainable than those on less fertile soils; the latter required more external inputs for achieving the same output, affecting most indicators negatively and reducing the feasibility for smallholders. Cassava and sweet sorghum performed similarly. Cassava production requires much more labour per hectare than production of sugarcane or sweet sorghum. Production of bioethanol feedstock on cultivated lands was more sustainable and had potential for carbon sequestration, avoiding GHG emissions from clearing natural vegetation if new land is opened.