In theory, greater interaction between researchers and practitioners should result in increased potential for implementation. However, we know little about whether this is the case, or what mechanisms might operate to make it happen. This paper reports findings from a study that is identifying and tracking implementation mechanisms, processes, influences and impacts in real time, over time in the Collaborations for Leadership in Applied Health Research and Care (CLAHRCs). This is a longitudinal, realist evaluation case study. The development of the conceptual framework and initial hypotheses involved literature reviewing and stakeholder consultation. Primary data were collected through interviews, observations and documents within three CLAHRCs, and analysed thematically against the framework and hypotheses. The first round of data collection shows that the mechanisms of collaborative action, relationship building, engagement, motivation, knowledge exchange and learning are important to the processes and outcomes of CLAHRCs' activity, including their capacity for implementation. These mechanisms operated in different contexts such as competing agendas, availability of resources and the CLAHRCs' brand. Contexts and mechanisms result in different impact, including the CLAHRCs' approach to implementation, quality of collaboration, commitment and ownership, and degree of sharing and managing knowledge. Emerging features of a middle range theory of implementation within collaboration include alignment in organizational structures and cognitive processes, history of partnerships, responsiveness and resilience in rapidly changing contexts. CLARHCs' potential to mobilize knowledge may be further realized by how they develop insights into their function as collaborative entities.