Collaborations between clinical investigators and behavioral and social science researchers (BSSR) produce many benefits, but also may generate challenges and complexities. Ongoing relationships between teams may affect the research carried out by the BSSR team and the way they interpret their findings. Here we describe our experiences conducting the HIV Remission (‘Cure’) Trials Decision-Making Study (DMS), in Thailand; these trials include potentially risky interventions and interruption of standard antiretroviral treatment, with little personal benefit. The DMS is a longitudinal study of the experiences of individuals recruited to such early-phase trials, and conducted alongside these trials. It originated in clinical investigators’ concerns about the ability of those recruited to make voluntary and informed decisions about scientifically complex studies, and is led by an independent group of BSSR and ethics researchers. In conducting this study, we experienced three overarching challenges to achieving a successful and dynamic collaboration: managing emerging findings as data were collected alongside clinical trial participation; evolving interconnectedness and shifting partnership boundaries among investigators; and the process of incorporating new research questions. By describing these challenges, we provide experiential evidence on how to manage multidimensional aspects of these collaborations. We describe how our research teams came together as well as the challenges and opportunities we experienced along the way. Our aim is to raise awareness of the scientific, practical, and ethical complexities of establishing and maintaining this kind of broad multidisciplinary collaboration over time. By describing our experiences, we hope to advance an agenda for others who undertake similar partnerships.