Eco-innovation methodologies and tools are being applied in companies to an increasing extent. None of them, however, are particularly adapted to complex systems industries, where the eco-design requirements are highly specific. These systems are characterized by large size and mass, and relatively long and uncertain life cycles. The associated organization is also complex as there are multiple highly specialized experts, who rarely collaborate, and much less so on environmental aspects. In this paper, an adapted eco-innovation process based on the eco-design strategy wheel is proposed for use with a working group of internal technical experts. A first phase involves generating a high number of potential eco-innovative R&D projects that are then analyzed and assessed using an appropriate multi-criteria grid. Three structured filters enable an informed selection of the most promising projects that will then make up a balanced R&D project portfolio. The whole process has been successfully applied at Alstom Grid on large electrical stations used in the primary aluminium industry.