While interdisciplinarity has been widely addressed in higher education policies and university strategies across countries, universities and colleges are struggling with the implementation at the programme level. For instance, extant literature implies many barriers to establishing interdisciplinary degree programmes (IDPs). However, there is a lack of both conceptual understandings and empirical investigations on how these barriers can be resolved through appropriate management. Our paper addresses this research gap by constructing an analytical framework for understanding the cause of barriers in the context of establishing IDPs and managerial approaches to overcome them through the lens of managing organisational innovation, and applying it in an empirical study of two cases of establishing IDPs at a Finnish research university. Our study yielded four conceptualised and tested propositions on key factors that middle-level university managers should consider for both preventing and resolving barriers to establishing IDPs. It suggests that while managers should plan IDPs that largely fit the institutional environment and bring foreseeable benefits to participants in the programmes, the art of their management lies in leveraging all relevant resources to enhance institutional compatibility, to change peoples' perceptions about profitability and to empower other participants' agency.