The recent proliferation of Massive Open Online Courses (MOOCs) has initiated a plethora of research endeavors revolving around new pedagogical methods in higher education. Integrating MOOCs in blended learning can be beneficial in different ways for both learners and instructors. In this position paper, we aim to provide a brief and comprehensive review about the challenges that higher education institutions in Macedonia and Kosovo face while coping with the new trends of flexible or blended learning. Moreover, after describing some real cases of MOOC based flipped classroom learning, we also provide some recommendations in order to enhance and enrich learning experience by employing innovative pedagogies.