Despite the extent and importance of the Smart Specialization strategies, achieved in a short cohesion policy period from 2014 to 2020, the evidence on the assessment of their actual effect on the economic development and the mobilization via the Smart Specialization implementation of the regions is still pending. In light of green transformation, accelerated by the European Green Deal, the heart of Smart Specialization strategies of EU regions is to avoid fragmentation and to reach a complementary in reaching the joint EU ambition of climate neutrality by 2050. This article aims to demonstrate how to identify the region-specific (place-based and bottom–up) pathways for green transformation and align them with the European Green Deal-focused Smart Specialization strategies in regions, using moderated co-creation in DPSIR analysis and policy modeling. The findings of this article are based on the moderated experimental experience from the two interconnected projects in the area, i.e., “LARS” and “GRETA”, implemented in the Baltic Sea Region (October 2017 to September 2021). The research proposes how moderated learning and knowledge transfer between matured innovators and young innovators embodies the identification of place-based pathways and help develop political course recommendations for green transformation, thus solving the homogeneity issues of the Smart Specialization strategies.