Partnering across health clinics and community organisations, while worthwhile for improving health and well-being, is challenging and time consuming. Even partnerships that have essential elements for success in place face inevitable challenges. To better understand how cross-organisational partnerships work in practice, this paper examines collaborations between six primary care clinics and community-based organisations in the United States that were part of an initiative to address late-life depression using an enhanced collaborative care model (Archstone Foundation Care Partners Project). As part of an evaluation of the Care Partners Project, 54 key informant interviews and 10 focus groups were conducted from 2015 to 2017. Additionally, more than 80 project-related documents were reviewed. Qualitative thematic analysis was used to code the transcripts and identify prominent themes in the data. Examining clinic and community organisation partnerships in practice highlighted their inherent complexity. The partnerships were fluid and constantly evolving, shaped by a multiplicity of perspectives and values, and vulnerable to unpredictability. Care Partners sites negotiated the complexity of their partnerships drawing upon three main strategies: adaptation (allowing for flexibility and rapid change); integration (providing opportunities for multi-level partnerships within and across organisations) and cultivation (fostering a commitment to the partnership and its value). These strategies provided opportunities for Care Partners collaborators to work with the inherent complexity of partnering. Intentionally acknowledging and embracing such complexity rather than trying to reduce or avoid it, may allow clinic and community collaborators to strengthen and sustain their partnerships.