The role of multilateral donor agencies in global health is a new area of research, with limited research on how these agencies differ in terms of their governance arrangements, especially in relation to transparency, inclusiveness, accountability, and responsiveness to civil society. We argue that historical analysis of the origins of these agencies and their coalition formation processes can help to explain these differences. We propose an analytical approach that links the theoretical literature discussing institutional origins to path dependency and institutional theory relating to proto institutions in order to illustrate the differences in coalition formation processes that shape governance within four multilateral agencies involved in global health. We find that two new multilateral donor agencies that were created by a diverse coalition of state and non-state actors, such as the Global Fund to Fight AIDS, Tuberculosis and Malaria and GAVI, what we call proto-institutions, were more adaptive in strengthening their governance processes. This contrasts with two well-established multilateral donor agencies, such as the World Bank and the Asian Development Bank, what we call Bretton Woods (BW) institutions, which were created by nation states alone; and hence, have different origins and consequently different path dependent processes.