Health within the sustainable development goals is regarded as holistic; hence for its successful realization across the globe, relevant policy action at the local levels is required to define country-specific targets focusing on leaving no one behind. Community-based initiatives provide an appropriate framework to position the direction of global health milestones to fall within the national policy agenda, in a more responsive, inclusive, socially acceptable and participatory manner. Nonetheless, considering the dynamic nature of community health, commonly used case study methods may fail to fully respond to such complexities and in a more systems-centric style—that is, may present problems in a more narrow and linear manner which in turn may affect proper decision-making. This case presents how we designed and conducted a stratified multistage case study, to capture the series of ongoing dynamics plus the long-standing fates of programs and factors influencing the Community-Based Health Planning and Service initiative in Ghana. We anticipate this study design could serve as a roadmap to help researchers and policy makers to identify and respond to the growing complexities of community health systems, for appropriate policy action.