Background: Collaborative multi-site research is gaining recognition. In particular, across stakeholders in the health and social care professions, there has been an increase in the documentation of such approaches, with the majority acknowledging the strengths and few identifying the pitfalls. Four universities in the south west of England collaborated on the design, analysis and implementation of a project scoping the staff development needs of nursing and midwifery academics to meet the National Health Service Modernisation Agenda in the United Kingdom. Aim: This paper highlights the challenges and the lessons learned from each stage of the process of this large multi-site collaborative study. Consideration has been given to addressing the site-specific differences as well as the politics of the processes and power relations across the research team. Discussion: From an analytical reflection across the team, there were a number of lessons learned from the process of collaboration. Initially, the main challenge was the selection of the team and lead researcher and these were its greatest success. Nevertheless, managing each individual's competing roles within the organisation remained problematic. Particular challenges included gaining consensus on the research design, the chosen sample and data collection to reflect the site-specific differences and were overcome through discussion and effective leadership. Towards the end of the study, adequately representing each institution in the findings, as well as dissemination have remained the greatest challenges. Conclusions: While collaboration has been lauded as a way forward, this analysis of the process highlights some of the difficulties of working as a multi-site virtual team who are widely spread geographically and who have no previous connection. At different stages of the process there has been acknowledgement of the political dimensions affecting such an approach and a need to avoid the pitfalls of collaborative working in order to harness the potential of all team members, if success is to be achieved.