Climate change mitigation is the most important driving force for bioenergy development. Consequently, the environmental design of bioenergy value chains should address the actual savings of both primary energy demand and greenhouse gases (GHG) emissions. According to the EU Renewable Energy Directive (2009/28/EC), no direct impacts and no GHG emissions should be attributed to crop residues (like cereal straws) when they are removed from agricultural land for the purpose of bioenergy utilisation. The carbon neutral assumption applied to crop residues is, however, a rough simplification. Crop residues, indeed, should not be viewed simply as a waste to be disposed, because they play a critical role in sustaining soil organic matter and therefore have an inherent C-capturing value. Moreover, considering straws as an energy feedstock, its status of co-product is clearly recognised and its availability could be obtained according to different cropping systems, corresponding to different primary energy costs and GHG emissions. This paper highlights some hidden features in the assessment of agricultural energy and carbon balance, still very difficult to be detected and accounted for. Although they are frequently disregarded, these features (such as long term dynamic trend of soil organic carbon and annual nitrous oxide emissions from the soil) should be carefully considered in assembling the energy and emission balance. By using a crop simulation model, the long-term soil organic matter and annual N2O soil emissions were estimated. Consequently, a comprehensive energy and GHG balance was determined in accordance with the life cycle assessment methodology. Contrasting methods of straw management and wheat cultivation were compared: straw retention vs removal from the soil; conventional vs conservation tillage; wheat cropping system as a single-crop or in rotation. The resulting carbon footprint of straws has different magnitudes with respect to the several experimental conditions. By selecting the best agricultural practices, energy from straw can be optimally coupled with grain productions, without detrimental effects on soil fertility. An improved and specifically tailored cropping system is designed to obtain an optimal trade-off. © M. Monteleone et al., 2015.