Community empowerment interventions, which aim to build greater individual and community control over health, are shaped by the community systems in which they are implemented. Drawing on complex systems thinking in public health research, this paper discusses the evaluation approach used for a UK community empowerment programme focused on disadvantaged neighbourhoods. It explores design choices and the tension between the overall enquiry questions, which were based on a programme theory of change, and the varied dynamic socio-cultural contexts in intervention communities. The paper concludes that the complexity of community systems needs to be accounted for through in-depth case studies that incorporate community perspectives.