The Sustainable Development Goal of universal health coverage, coupled with the withdrawal of international donors in a growing number of countries, has underscored the need for resource prioritisation in the health sector in low- and middle-income countries. These shifts pose not only a financing challenge but also an institutional one. In this paper, profiles of Laos, Liberia and Kenya illustrate the different challenges countries were facing in 2019 and the complex institutional landscapes involved in health financing decisions. We identify three key domains where more targeted attention could be directed when developing donor transition strategies, when strengthening national decision-making processes, and in future research. These are the interfaces between (1) domestic and international financing, (2) national planning and budgeting, and (3) central and subnational levels of government.