Higher education institutes both foster the advancement of knowledge and address society's socioeconomic and environmental challenges. To fulfil these multiple missions requires significant changes to how the role of a researcher is perceived e.g. a researcher identity that is congruent with the objective of contributing to fundamental knowledge while also engaging with non-academic actors, broadly, and entrepreneurship, in particular. We argue that the early stages of an academic career—namely the PhD training trajectory—and the knowledge networks formed during this period have a major influence on the scientist’s future capacity to develop an appropriate researcher role identity. We draw on knowledge network and identity theories to investigate how the knowledge networks (i.e. business, scientific and career knowledge networks) of PhD students promote changes to, reinforce or conflict with the perception of a researcher role identity. Our longitudinal qualitative network study includes PhD students and their supervisors funded by the H2020 FINESSE project. At the network level, we show that scientific knowledge is distributed equally throughout young academics’ networks but that entrepreneurial (business) and career knowledge tend to be concentrated around certain individuals in these networks. On the PhD student level, we observe different pronunciations of the researcher role identity linked to students’ interactions with their knowledge networks. We distinguish identity conflicts due to misalignment between ego and alters which leads to withdrawal from the network. Our findings have practical implications and suggest that universities and PhD student supervisors should support PhD students to develop a researcher identity which is in line with the individual PhD student’s expectations.