Abstract Background This paper argues that the global health agenda tends to privilege short-term global interests at the expense of long-term capacity building within national and community health systems. The Health Systems Strengthening (HSS) movement needs to focus on developing the capacity of local organizations and the institutions that influence how such organizations interact with local and international stakeholders. Discussion While institutions can enable organizations, they too often apply requirements to follow paths that can stifle learning and development. Global health actors have recognized the importance of supporting local organizations in HSS activities. However, this recognition has yet to translate adequately into actual policies to influence funding and practice. While there is not a single approach to HSS that can be uniformly applied to all contexts, several messages emerge from the experience of successful health systems presented in this paper using case studies through a complex adaptive systems lens. Two key messages deserve special attention: the need for donors and recipient organizations to work as equal partners, and the need for strong and diffuse leadership in low-income countries. Summary An increasingly dynamic and interdependent post-Millennium Development Goals (post-MDG) world requires new ways of working to improve global health, underpinned by a complex adaptive systems lens and approaches that build local organizational capacity.