In 2016, 1100 million people lack access to electricity, mainly in developing countries in Africa, Asia and South America. In these countries, there is a large potential for hydroelectric production through off-grid microgrids, although not fully exploited. This work assesses the long-term sustainability of off-grid micro-hydro projects operating in rural indigenous communities. More specifically, four sustainability dimensions are analyzed: environmental, technical, socioeconomic and institutional, and specific indicators are proposed for each one. In particular, 6 micro-hydroelectric power plants in southern Venezuela are used as case studies. The data gathering includes surveys, technical visits and interviews with technicians, engineers and beneficiaries. Results show that the institutional dimension and, in particular, alignment between involved institutions has been fundamental for the long-term sustainability. Indeed, appropriate institutional alignment is the key to strengthening the impacts on: (i) the environmental dimension, minimizing emissions and impacts on local ecosystems; (ii) the technical dimension, improving adequacy and reliability of technologies; and (iii) the socioeconomic dimension, making efficient use of electricity to enhance education, health and productivity. Lessons learned and conclusions of this research can significantly contribute to improve future projects, in particular to the 22 included in the electrification plans of Venezuela in coming years.