The integration of environmental concerns into the product design process is not trivial when dealing with complex industrial systems. Actually, environmental assessment methodologies like Life Cycle Assessments (LCA) reach, in this case, methodological and organisational limits. More generally, the complexity inherent in the design process may put off eco-design initiatives from a lack of organisational management, methods and tools. In this paper, we propose a project management methodology to facilitate the integration of eco-design into the design process of complex industrial systems. This methodology is based on continuous improvement and a DMAIC process. It is then structured around precise team definition, precise milestones, deliverables and phases. A first stage ensures a reliable environmental assessment of the full system and the identification of environmental improvement projects. A second stage allows the independent execution of the most promising improvement projects. A first application is proposed on the Alstom Grid AC/DC conversion substations for the aluminium industry. A Life Cycle Assessment has been performed with limited resources and has provided rich findings and promising perspectives. It shows in particular that the best environmental configuration of such a complex industrial system depends on external parameters like the implantation site.