The objective of this research is to understand how startups and established companies perceive the factors that are critical to the cooperation between them in the context of corporate incubation programs. We interviewed innovation managers, analysts, and project leaders from three large companies and the entrepreneurs of the startups that interacted with these companies. The results show that established companies and startups have different perceptions regarding insufficient dedication to the program and cultural differences, although both considered these factors to constrain the collaboration. Regarding motivation and incentives and autonomy, the findings were to some extent different. Implications include the difference in the perceptions of the startups and employees of the established companies directly involved in the program and the two factors identified as critical—dedication to the program and cultural differences—due to their potential to risk the incubation program. To practitioners, this research offers empirical results that can guide decision-making to manage corporate incubation programs.