To reduce greenhouse gas (GHG) emissions, the European Union (EU) has targets for utilizing energy from renewable sources. By 2030, a minimum of 3.5% of energy in the EU’s transport sector should come from renewable biological sources, such as crop residues. This paper analyzed EU’s “advanced bioethanol” potential from wheat straw and maize stover and evaluated its environmental (land, water, and carbon) footprint. We differentiated between gross and net bioethanol output, the latter by subtracting the energy inputs in production. Results suggest that the annual amount of the sustainably harvestable wheat straw and maize stover is 81.9 Megatonnes (Mt) at field moisture weight (65.3 Mt as dry weight), yielding 470 PJ as gross (404 PJ as net) advanced bioethanol output. Calculated net advanced bioethanol can replace 2.95% of EU transport sector’s energy consumption. EU’s advanced bioethanol has a land footprint of 0.28 m2 MJ−1 for wheat straw and 0.18 m2 MJ−1 for maize stover. The average water footprint of advanced bioethanol is 173 L MJ−1 for wheat straw and 113 L MJ−1 for maize stover. The average carbon footprint per unit of advanced bioethanol is 19.4 and 19.6 g CO2eq MJ−1 for wheat straw and maize stover, respectively. Using advanced bioethanol can lead to emission savings, but EU’s advanced bioethanol production potential is insufficient to achieve EU’s target of a minimum share of 3.5% of advanced biofuels in the transport sector by 2030, and the associated water and land footprints are not smaller than footprints of conventional bioethanol.