The European Green Deal adopted by the European Commission in December 2019 brought major opportunities to transform the EU’s Single Market for the net-zero age. Various partnerships focused on the green and digital transitions, engaging large numbers of stakeholders from different EU countries and regions, and from multiple economic sectors and institutions, have been actively promoted since 2020, receiving substantive EU funding to ensure the Single Market’s transition to the net zero economy. However, the impact of these partnerships on the Single Market remains largely unexplored. This paper aims to shed light on this aspect by looking at selected innovative partnerships in two key areas of the European Green Deal: Research and Innovation (financed through Horizon 2020 and Horizon Europe) and Cohesion policy (financed through Interreg Europe and the I3 instrument). The analysis was performed from an ‘innovation system’ perspective on the Single Market, and the innovation system ‘functions’ framework was used to identify partnerships’ effects on the industrial ecosystems, in terms of knowledge and technology generation and diffusion; market formation and growth; resource mobilisation, governance, and creation of legitimacy/counteracting resistance to change.