As a response to the complexity of reducing health inequity there has been a rise in community-based health promotion interventions adhering to the principles of complexity thinking. Such interventions often work with adaptive practice and constitute themselves in complex webs of collaborations between multiple stakeholders. However, few efforts have been made to articulate how complexity is experienced by stakeholders or can be addressed in practice. This study explores how partners experience and navigate complexity in the partnership behind Tingbjerg Changing Diabetes (TCD), a community-based intervention addressing health and social development in the disadvantaged neighborhood of Tingbjerg in urban Copenhagen. The study is based on 18 months of ethnographic fieldwork in the local community including participant observations and 9 in-depth interviews with key partner representatives. Findings show that complexity in TCD can be characterized by unpredictability in actions and outcomes, undefined purpose and direction, and differing organizational logics. Factors that support partners’ navigation in complexity include connectivity, embracing a flexible intervention framework, autonomy, and quick responsiveness. The study showcases the interdependency between the intervention and the context of the disadvantaged neighborhood of Tingbjerg and encourages stakeholders and researchers to embrace the messiness of complexity, and to pay attention to ways through which messiness and unpredictability can be handled.