The objective of this study is to identify, systematize and compare good practices in education in Ecuador and El Salvador (2 case studies from each country). In both countries the public sector in the main implementor of educational projects and initiatives, which generates limitations to implement new methodological approaches in this field. Civil society organizations (CSOs) play an essential role in educational innovation, evidence generation and providing attention to priority groups and areas. In the four cases reviewed, the support of partner organizations and CSOs with larger experience in Latin America, had a positive effect in the projects’ conceptualization, execution, the possible adaptations and the obtained results. The cases’ analysis has showed that one of the main challenges educational projects face are related to long term sustainability. In this sense, the importance of generating strong alliances and exchanges with the private sector has become more and more visible, specially in terms of financial sustainability. At the same time, these alliances allow to positioning “quality education” as a shared responsibility between different sectors. Furthermore, the paper articulates that when CSOs’ execute education projects and initiatives in countries like Ecuador and El Salvador, South-South cooperation plays an essential role, ensuring technical and methodological assistance.