The shift from straw incorporation to biofuel production entails emissions from production, changes in soil organic carbon (SOC) and through the provision of (co‐)products and entailed displacement effects. This paper analyses changes in greenhouse gas (GHG) emissions arising from the shift from straw incorporation to biomethane and bioethanol production. The biomethane concept comprises comminution, anaerobic digestion and amine washing. It additionally provides an organic fertilizer. Bioethanol production comprises energetic use of lignin, steam explosion, enzymatic hydrolysis and co‐fermentation. Additionally, feed is provided. A detailed consequential GHG balance with in‐depth focus on the time dependency of emissions is conducted: (a) the change in the atmospheric load of emissions arising from the change in the temporal occurrence of emissions comparing two steady states (before the shift and once a new steady state has established); and (b) the annual change in overall emissions over time starting from the shift are assessed. The shift from straw incorporation to biomethane production results in net changes in GHG emissions of (a) −979 (−436 to −1,654) and (b) −955 (−220 to −1,623) kg CO2‐eq. per tdry matter straw converted to biomethane (minimum and maximum). The shift to bioethanol production results in net changes of (a) −409 (−107 to −610) and (b) −361 (57 to −603) kg CO2‐eq. per tdry matter straw converted to bioethanol. If the atmospheric load of emissions arising from different timing of emissions is neglected in case (a), the change in GHG emissions differs by up to 54%. Case (b) reveals carbon payback times of 0 (0–49) and 19 (1–100) years in case of biomethane and bioethanol production, respectively. These results demonstrate that the detailed inclusion of temporal aspects into GHG balances is required to get a comprehensive understanding of changes in GHG emissions induced by the introduction of advanced biofuels from agricultural residues. The article evaluates changes in greenhouse gas (GHG) emissions arising from a shift from straw incorporation into agricultural soil to advanced biofuel production. The focus of the evaluation is set on the change in the temporal occurrence of emissions. The study shows that the provision of organic material can contribute to soil organic carbon formation and thereby increase net reductions in GHG emissions.