This chapter contribution to the edited volume addresses the growing interest among science policy researchers and practitioners in understanding the organisational dilemmas confronted in cooperative research centres (CRCs). The authors Sam Garrett-Jones, Tim Turpin and Kieren Diment acknowledge that little empirical evidence exists on (a) how individual researchers perceive the benefits of their participation, (b) how far the structures and functions of particular centres coalesce around of researchers’ expectations and (c) what problems arise for researchers who opt for a ‘second job’ in the centre. The authors use the broad policy and organisational context of the Australian CRC to conduct a qualitative analysis of a survey of respondents from government organisations and universities involved in these centres. They use the perspective of the individual research scientists from academia and government participating in centres to illuminate the management issues of trust, governance and competition between functional domains, which emerge from the field of inter-organisational relationships, which the authors suggest have been inadequately recognised in the context of CRC including but not limited to the Australian model. For complementary examinations, see the chapter by Branco Ponomariov and Craig Boardman on benefits across stakeholder types (including but not limited to academic faculty) from participation in CRC as well as the chapter by Beth M. Coberly and Denis O. Gray on the tangible and intangible benefits gained (or not) by academic faculty participating in centres.