This article draws on the case of academic work produced by Colombian scholars, to address the debate on the persistent failure of policy efforts to improve school effectiveness. Realist meta-theory plays a significant role in this research, because it provides a general framework to identify ontological problems and inconsistencies in empirical and theoretical positions informing policy debates in the country. The analysis focuses on the contributions and weaknesses of empiricism, structuralism and post-structuralism in the work of Colombian scholars, and concludes by arguing for the need to deploy research methodologies that study stratified emergent social processes behind observable educational outcomes.