Anchored on a systemic perspective of innovation and particularly on the triple helix model, which highlights the state, university and companies as central players, this paper aims to discuss the factors that enable or constrain the processes of innovation, using the system thinking approach to understand the academia-industry symbiosis. The paper’s empirical section is based on a case study on Portugal’s major highway management concessionaire. In order to ensure a “healthy” co-innovation environment, the archetype studied emphasizes the need to implement coordination mechanisms such as communication routines and metrics to monitor collaborative behavior in addition to the need to develop global goals that align the efforts of the partners.