The optimal use of food components in human nutrition is key to reduce the environmental burdens of the global food system. In this life cycle assessment (LCA) case study based on Greek yogurt (GY) production systems, we explore how a system boundary expansion approach (SBES), instead of an allocation approach, can help to optimize the use of the milk components in the dairy industry for the province of Québec, Canada. GY is a high-protein-low-fat dairy product considered as a healthy high-value product for human nutrition. Its production requires large volumes of milk and generates a high-value co-product (cream) and a by-product (whey). This comprehensive LCA study compares three production technologies (centrifugation (CE), ultrafiltration (UF) and fortification (FO)) and different whey management alternatives (animal feed, biogas and fertilizer production, waste treatment). Results show that, under current Canadian market conditions in which milk production is driven by the demand for cream and surplus non-fat-solids are downcycled on the animal feed market, the CE and UF technologies, which require more raw milk than FO and produce more cream, enable better synergies in the use of milk components and improve the environmental performance of GY as compared to FO. Both CE and UF make it possible to use the excess of Canadian milk proteins in human nutrition, in compliance with circular economy principles. In this respect, neither the quantity of whey generated, nor the whey management pathway significantly influence the GY environmental footprint.