In the digital transformation era, especially university-based innovation ecosystems (IEs) play an essential role in linking science and technology universities with industrial firms, including startups and enterprises. However, establishing a productive collaboration between these actors has many challenges. In this context, we primarily aim to explore the roles of universities as strong IE actors in Industry 4.0 technologies domain from the view of startup companies in these ecosystems. This article devises an integration matrix framework that links the I4.0 technology domains and their adoption challenges with the universities' roles and obstacles for contributing to I4.0 adoption and digital transformation. The proposed framework considers and integrates the opinions of different stakeholder groups for prioritizing issues to select high-impact policy areas for universities. We collect data on the prioritization and links between the framed technologies, their challenges, universities' roles, and obstacles by performing two different Delphi studies with 59 cofounders of Industry 4.0 startups and 15 experts on IEs in Turkey, as a case from developing country context. The integration matrix indicates high-impact and priority areas for policy development from a complex dataset, reflecting the voices of IE stakeholders in a structured way. The study also discusses the theoretical and managerial implications of the findings, highlighting potential research.