Researchers and policymakers increasingly aim to set up collaborative research programmes to address the challenges of adaptation to climate change. This does not only apply for technical knowledge, but for governance knowledge also. Both the Netherlands and Germany have set up large-scale collaborative action research (CAR) programmes for the governance of adaptation to climate change. Despite the collaborative designs, the initial enthusiasm, the available resources and the many positive outcomes, both programmes encountered several stubborn difficulties. By comparing both programmes, this paper explores the difficulties researchers encounter, analyses the underlying mechanisms and presents some lessons. It found that many difficulties are related to the tensions that exist between the assumptions underlying the new collaborative trajectories and the logics of the existing policy and research institutions. These institutional misfits are decisive to explain ultimate difficulties and successes. Furthermore, the paper concludes that risk aversion, stereotyping and scale fixation strengthen institutional misfits; and that these misfits persist due to lacking bridging capabilities. We suggest some lessons that can help to resolve the difficulties and reconcile CAR into existing institutions: organize the knowledge arrangement as a collaborative process; construct boundary objects as focal point for collaboration; and invest in bridging capabilities.