Greek yogurt (GY), a high-protein-low-fat dairy product, particularly prized for its sensory and nutritional benefits, revolutionized the North American yogurt market in less than a decade, bringing with it new sustainability challenges. The standard production of GY generates large volumes of acid whey, a co-product that is a potential source of environmental pollution if not recovered. This study aims to assess the environmental performance of different technologies and identify the main factors for improving GY production. A complete life cycle assessment (LCA) was performed to compare the standard technology (centrifugation) with two new technologies (fortification and ultrafiltration) to reduce acid whey volumes. Three milk protein concentrate alternatives were also assessed. Results show that the technology choice is not a clear discriminant factor. However, minimizing losses and wastage (accounting for 23 to 25% of the environmental impacts for all indicators) beyond the processing plant and selecting milk ingredients (accounting for 63 to 67% of the impacts) with low environmental impacts are key factors in improving the environmental performance of GY systems. From a methodological perspective, the results also highlight a shortcoming in the current International Dairy Federation LCA guidelines (2015) for treating the multifunctionality of GY systems.