The main objective of this study is to better understand the challenges of transdisciplinary knowledge production processes and its institutionalisation at universities. Transdisciplinary research is considered a collaborative and integrative praxis grounded in different ways of knowing, acting and being. However, transdisciplinary research practices differ significantly in the relations between institutions and actors. These differences have an impact on how transdisciplinarity is institutionalised. There is a need to incorporate them into a larger framework of ongoing transformations of scientific timescales and spaces at universities. We present the results of a case study developed at Babes-Bolyai University (Romania). We discuss it against the background of three models of transdisciplinary knowledge production and two approaches of transdisciplinary problem-solving research. We apply a qualitative methodology of micro level analysis that explores research practices and their embeddedness in the institutional environment. We analyse conditions that enable transdisciplinary knowledge production and show how transdisciplinary institutionalisation can be better understood using the proposed framework applied to the case study. It could be shown that taking into consideration the differences in the models of transdisciplinary knowledge production proved to be useful to gain a deeper understanding of processes of institutionalising transdisciplinarity at universities.