Large scale, multi-organisational collaborations between researchers from diverse disciplinary backgrounds are increasingly recognised as important to investigate and tackle complex real-world problems. However differing expectations, epistemologies, and preferences across these teams pose challenges to following best practice for ensuring high-quality and rigorous qualitative research, while maintaining goodwill and team cohesion across team members. This article presents critical reflections from the real-world experiences of a team navigating the challenges of collaborating on a large-scale, cross-disciplinary interview study. Based on these experiences, we extend the literature on large team qualitative collaboration by highlighting the importance of balancing autonomy and collaboration, and propose eight recommendations to support high quality research and team cohesion. We identify how this balance can be achieved at different times: when centralised decision-making should be prioritised, and autonomy can be allowed. We argue that prioritising time to develop shared understandings, build trust, and creating positive environments that accept and support differing researcher perspectives on qualitative methods is paramount. By exploring and reflecting on these differences, teams can identify how and when to support autonomy in decision-making, when to move forward collaboratively, and how to ensure that shared processes reflect the needs of the whole team. The reflexive findings, emanating from practical experience, can inform large research teams undertaking qualitative studies to explore complex issues. We make an original contribution to qualitative methods research by arguing that balancing autonomy and collaboration is the key to promoting high quality research and cohesion in large teams.