The process of European integration is being challenged by the rising heterogeneity of European member states and policies. As a consequence the European Union supports the differentiated deepening of integration through flexible, soft governance instruments which enable cooperation despite heterogeneity. For implementing the European regional policy, regions across Europe voluntarily cooperate in thousands of Interreg-projects. Based on a qualitative social network analysis of an Interreg project within the field of the European innovation policy, this work shows that inter-regional learning and cooperation lead to a differentiated Micro-Integration of Europe. By overcoming the geographical and structural distances between regions, inter-regional projects function as platforms for functional policy learning between regional policy-makers. Based on joint interests functionally differentiated spaces of deeper Micro-Integration are being established throughout Europe.