The purpose of the doctorate and the desirable outcomes of doctoral education are the focus of debates in the UK, the USA, Australia and other Organisation for Economic Development countries. Part of that reconceptualisation of the doctorate includes a growing international interest in university–industry research, which, as a consequence, has become one of the emergent features of contemporary doctoral programs. This article, which draws on findings from a research study in an Australian university, focuses on the impact of university–industry research on the process and practice of doctoral supervision, and in particular the pedagogical, epistemological and institutional issues being faced by doctoral supervisors. Doctoral supervisors interviewed were positive about the benefits of university–industry research, but they also identified areas of changing practice and of dissonance. Individual personal skills were an important feature in developing positive collaborative partnerships. Given current national and international priorities for a nexus between university and industry research, this study illustrates the need for a stronger pedagogical, epistemological and institutional framework that is mutually beneficial for both universities and industries in research partnerships.