Greek-style yogurt is characterized by a higher protein content (>10% w/v) compared with conventional products (4–5% w/v). The protein concentration is typically achieved by ultrafiltration (UF) or centrifugation processes after milk fermentation by yogurt starter cultures. However, this approach requires 3 times more milk than the traditional yogurt and it generates Greek yogurt co-product acid whey permeate for which the subsequent valorization represents a challenge. Although the concentration step increases the commercial value of yogurt, depending on the processing options selected, its manufacture affects the use of milk constituents and on the process environmental footprint. The concept of eco-efficiency (EE) provides an assessment of the environmental performance of a product system in relation to its value. EE is a practical tool for managing environmental data (e.g., Life cycle analysis or LCA) and value aspects (e.g., financial, functional, sensory) in parallel. In a first part of our study, we have compared the environmental impact of Greek-style yogurt production from 2 different processing options, i.e., performing the UF concentration step before or after fermentation step. Pilot-scale experiments were performed to characterize both processes in terms of water use, energy consumption and waste generation such as permeate (acid or not). The relative environmental impact of both processes will be characterized by means of a comparative LCA. The value aspects of Greek-style yogurt manufacture in the EE equation will address its direct commercial value, but also the value (or costs) of co-products valorization (or disposal). Our research aims at developing an EE-based approach and provide a decision-support tool to help manufacturers identifying and selecting most eco-efficient processing options for the production of Greek-style yogurt.