Innovation has come a long way since the times it was defined just as a new idea. Nowadays, innovation activities comprise a lot more, from new products and/or services to improvements in organisational business models. The healthcare sector is no exception. This leads public authorities to increase their investment in innovation, research and development in the healthcare sector. The rising of internal and external collaborations between hospitals and other parties calls for a specific analysis on how the healthcare innovation environments behave and how knowledge flows within them are managed. This study, through the lens of the ecosystem theory, aims to study how a healthcare innovation ecosystem can be activated and knowledge flows are managed to ensure that all the parties are benefited. For that purpose, it presents a case study based on a set of three meetings of Portuguese stakeholders inserted in innovation healthcare ecosystems. With this work it was possible to observe that the healthcare innovation ecosystem can be analysed from different perspectives. The interaction with the different stakeholders allowed to identify possible partners to be involved in innovation activities (e.g.: hospitals, universities, research centres, start-ups). This paper suggests possible roles for the different parties along the innovation funnel as well as what they can do in each phase. Using a case study approach, it is possible to compare different contexts and identify best practices on the management of healthcare innovation ecosystems. Also, it becomes evident the need for more effective knowledge management to ensure that hospitals and the other parties meet their goals and play a relevant role in the ecosystem. Although this paper provides guidelines for action, it lacks implementation of the suggestions in a specific context. As such, this paper aims to serve as a basis for future research on the study of hospitals’ innovation ecosystems and underlying knowledge flows, in different contexts to achieve best practices for its effective management.