Natural resource-based innovations (NRBIs), especially through the valorization of waste and side streams, have recently become a significant element of the bioeconomy agenda in several countries across the world. Accordingly, a variety of institutions, including universities, have been expected to contribute to such innovations. While there have been serious efforts within universities to play a key role in NRBIs, questions of the extent of institutional continuity of these efforts over time and how this can be achieved remain unanswered in the literature. This paper, therefore, seeks to identify the determinants of a highly institutionalized structure that is supportive of NRBIs in universities. By mobilizing a literature in which the level of structuration is conceptualized as the degree of institutionalization and by using a single case study of a Portuguese public university, it was found that several internal and external factors have contributed to the institutionalization process, which has led to the emergence of a sedimented structure. Despite a high degree of institutionalization, several challenges that have either impeded the harnessing of the full potential of NRBIs or that have posed a threat to the university’s highly institutionalized structure were also found. The paper concludes that the institutionalization of NRBIs within universities not only requires orchestrated organizational efforts but also more consideration of the social, economic, and political dynamics that have recently engulfed universities.