This research aimed to investigate how the governance structure of innovation habitats may contribute to the development of innovation in resident companies. An exploratory study was conducted in INOVAPARQ and CELTA incubator, in Brazil. The empirical contexts were investigated by applying qualitative method with NVivo software. Critical success factors of governance were found: managerial relationships with different stakeholders; national and international training networks; and boosted resident companies monitoring by specific assessment tools. It was concluded that these factors are crucial to the innovation process of resident companies mostly by creating new products and services; sharing of inter-company knowledge; and motivating employees to work in a creative environment.