In the context of strengthening sustainability of production systems, agri-food products become the target of environmental evaluation using life cycle assessment (LCA°. Most of agri-food production systems include multifunctional processes, a common challenge occurs regarding the way to partition impacts among co-products. This is known as the allocation problem. Many approaches have been introduced, leading to different results. One major question that LCA practitioners face is the allocation method choice. The extensive literature review achieved in this study allowed the identification of the most used and acknowledged allocation methods. A cross-analysis unveiled a strong link between allocation choice and decision-makers’ objectives. Hence, this paper proposes to identify the LCA scope, and to use a contextual reasoning to choose the allocation method. These findings were tested on two LCA studies involving agri-food co-products: deteriorated apples and wheat straw. It was validated and discussed in line with the ISO 14044:2006 guidelines.