Many industrial food processes are multi-steps, multi-products systems, and sharing the environmental impacts produced by each step to each product is critical when implementing life cycle assessment (LCA) method. The objective of the study was therefore to investigate subdivision and different allocation rules as means of accounting for branched process itineraries such as the fractionation of milk into cream, casein, whey proteins and lactose as a case study. Depending on the mass, dry matter, protein or economic allocation, single products may or may not bear significant environmental impacts, thereby stressing the need for equally detailed inventories for all co-products. Aggregating the results by step or by input further helps identifying hotspots. Methodological choices in LCA of multifunctional systems are therefore strategic decisions that ultimately affect the eco-design of products, processes and food chains.