Vulnerable sectors of the population living in poverty in developing countries are highly dependent on renewable natural resources for their livelihoods and daily lives. Sustainable resource management, improving the well-being of vulnerable people, and building resilience to shocks are global challenges. This study analyzed the outcomes of various autonomous innovations by the people themselves and the enablers of these innovations in the communities of developing countries. This analysis of 20 autonomous innovations from six countries revealed that these innovations produced outcomes that simultaneously improved multiple indicators of human well-being, including “basic materials for a good life”, “safety”, “health”, and “good social relations”. The process of promoting public values, such as education, health improvement, and landscape conservation as a by-product of collective actions was an important enabler of these innovations, as well as the innovator’s proactive attitude toward continuous improvement. Public values and supporting ecosystem services were emphasized from the early stages of collective actions, to realize synergies toward integrated natural resource management. It is also important to achieve conditions in which collective actions could be practiced autonomously and adaptively. These results revealed the great potential of autonomous innovations emerging among socially vulnerable groups and the important mechanisms for promoting autonomous innovations for the transformation of social-ecological systems toward sustainable futures.