Joint Ph.D. projects are a prominent form of research collaboration, connecting universities to firms and public research organizations. When entering into such collaborations, partners need to make choices regarding a project’s governance. This paper investigates how a university and its partners govern such projects, including decision-making, daily management and disclosure policies. Earlier studies show that shared governance modes have had a higher success rate than centralized governance modes. Nevertheless, more than two thirds of the 191 joint Ph.D. projects we investigated opted for centralized rather than shared governance. Our findings show that: (1) geographical and/or cognitive distance render the adoption of a shared governance mode less likely; (2) the partner controlling critical resources tends to centralize governance, and (3) partnering firms are more likely to put restrictions on publication output than public research organizations. We therefore recommend that universities and their partners take these aspects into account when selecting such projects.