Research and innovation have been acknowledged as one of the nine interlinked and mutually reinforcing drivers of Single Market’s sustainable competitiveness. Specific KPIs have been introduced to assess progress, but they have some limitations both in number and in scope. To better capture the impact of the European Green Deal, we propose an ‘innovation system’ perspective of the EU Single Market, centred on its quintessential structural element—the industrial ecosystem. The industrial ecosystems are themselves a set of interconnected sectoral and technological innovation systems that can be analysed using the seven functions of an innovation system as an exploratory tool.