The introduction of interdisciplinarity and industry-academia collaborations (IAC) into higher education institutions (HEIs) and curricula as tools for promoting sustainable development has been debated both in academic and non-academic contexts. While overall rising trends in the acceptance of interdisciplinarity and IAC exist, research has stressed difficulty in implementation and practices. We conducted eight focus groups at six European Universities (members of the SEA-EU alliance) and analysed the transcripts using Braun and Clarke’s reflexive thematic approach to qualitative analysis in order to develop themes on barriers and facilitators to both conducting interdisciplinarity and IAC, as well as the inclusion of university students in interdisciplinary research. We observed that the main barriers to IR and IAC and the inclusion of students in such activities include traditional HEI structures focused on single-discipline approaches, a lack of joint platforms for IR and IAC, and academic differences (publication outcome differences, academic background). Likewise, a lack of funding (especially for early career researchers), employability (for students willing to do a research career), and a lack of validation by HEIs for researchers conducting IR and IAC are major barriers. To IDR- and IAC-related activities, a top-down approach is needed to restructure HEIs and make them more accommodating to both students and staff willing to conduct IR and IAC activities, thus refocusing them towards sustainability.