Cooperative research centres are a well-established organizational embodiment of the ‘triple helix’. As complex inter-organizational structures they are subject to diverse management strategies. The imperatives that drive their strategic plans and their impact on partner organizations and the careers of the scientists who work within them are not well understood. We examine 370 participants’ experience in Australian Cooperative Research Centres and consider their effect on personnel and organizations in the public research system. We propose that a necessary part of management strategies is the negotiation and reconciliation of risk and reward for partner organizations and careers of participating scientists. Achieving a sustainable strategy carries implications for change within the partner organizations and for the endurance of CRCs as organizational arrangements. These emergent triple helix structures can be harbingers of change not just for the alternative institutional structures they present and the partner organizations, but also for the careers of scientists.