Background Hydropower is a mature energy technology and one that could play a more important role in providing clean and reliable energy. In small-scale contexts, hydropower is useful for providing electricity access, balancing intermittent resources, and as a potential source of energy storage. This paper provides a comprehensive exploration of the development of the small hydropower (SHP) sector in Indonesia, the world’s fourth most populous country. Methods Two research methods were employed: secondary data analysis through a desk review of relevant literature and primary data collection through site visits and expert and stakeholder interviews. Two case studies of micro-hydro applications in community-based rural electrification were analyzed. The paper explores how SHP projects were initiated, lessons learned, and policy recommendations of relevance to further development of distributed small-scale renewable energy in Indonesia. Results The sector commenced during the Dutch Era and now centers on both community-based rural electrification projects and commercial schemes under the independent power producer (IPP) approach. Since the late 1980s, initiatives to implement SHP for rural electrification have flourished through various programs. Key regulatory, economic, and technical barriers include inconsistent and unclear supporting regulations, especially regarding electricity prices; artificially low retail electricity prices; capital and borrowing constraints; advantages provided to fossil fuels; limited technical experience and capabilities of project developers and project sponsors; risks from floods, earthquakes, and landslides; constraints on supporting infrastructure; and limited grid links. The most successful and sustainable SHP projects are ones that provide local economic benefits and for which local communities are empowered with ownership and have responsibility for maintenance. Conclusions SHP will remain small from a macro perspective but could still play a key role in further improving energy access and equity in remote areas. Key initiatives to facilitate this development could include local-level capacity building and project participation and the adequate pricing of negative externalities from fossil fuel projects. Indonesia’s long experience with SHP carries lessons for other developing countries.