In this chapter, the analytical framework of innovation system functions is applied to assess the impact of the European Green Deal on the Single Market industrial ecosystems. Several indicators and activities selected from multiple sources are used to explore each function across the 14 industrial ecosystems. The findings reveal an ample impact of the European Green Deal on the Single Market’s industrial ecosystems. However, the uneven concentration of R&I projects and EU R&D funding for the green and digital transitions across the ecosystems may have the unintended effect of creating new imbalances at the level of the Single Market as a whole, and affect the economic performance and capacity of the ecosystems with low levels of such investments to implement green and digital technologies in the longer run. This deficit is compensated to a limited some extent by the indirect benefits derived from the economic links with the other ecosystems and the investment provided through other instruments, such as the Recovery and Resilience Plans.