The innovation literature is growing rapidly and one of the of the main concerns is about the contexts that encourage and strengthen the results of innovation. Researches on innovation environments are still in its early stages. This paper sheds light on the process of fostering and developing an innovation ecosystem in cities with the perspective of institutional work, considering the need to institutionalize the collaboration. The method used was a multiple cases study, in a descriptive and processual approach. The study was conducted in two cities in Latin America: Porto Alegre and Florianopolis. The findings are that there is a logic in the process of institutionalization of collaboration that reflects on the development of the innovation ecosystem, which occurs in three phases involving three groups of actors: leaders, support and community. Understanding this process can help other cities or regions to promote their own innovation ecosystems.