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This paper highlights the main questions that were at the core of the seminar “Transdisciplinary Research in the Universities” held on September 14, 2018 at the Université Libre de Bruxelles. By producing hybrid scientific and socially relevant knowledge, transdisciplinary research contributes actively to social change and thus fulfills the major academic missions of research and contribution to society. However, transdisciplinary research suffers from a lack of recognition of its methodological rigor and scientific validity by the academic establishment. Taking this observation as an urgency, the seminar provided debate and reflection on the challenges specific to the implementation of transdisciplinary research in academic institutions: the legitimacy of the knowledge produced, the evaluation of the scientists’ practice, and funding. This paper highlights the current obstacles and presents a concise overview of the reflective solutions generated during our debates. It also proposes some ideas that can support the full development of transdisciplinarity.