The European University Initiative touches on many different aspects of higher education – from student mobility to innovative skills teaching, to inclusion procedures. This policy paper explores two major areas where European University Alliances are actively driving transformation in the European Education Area, and examines some of the related implementation barriers, namely 1) Micro-credentials and other joint short-term learning offers, and 2) Short-term and virtual mobility. The paper elaborates how we need to consider a European approach to micro-credentials and virtual and short-term mobility from the beginning and urges national policy makers to take the needs of the European Alliances into consideration when addressing issues around accreditation, quality assurance, student status and funding mechanisms. Continued institutional efforts to address the challenges identified here can only be successful with this complementary change at national and European levels. .