This paper studies the incidence of the Colombian armed conflict on the academic performance of secondary students at the municipal level for the years 2003 and 2017. By using a General Nesting Spatial model, results suggest the conflict negatively affects academic performance. In 2003, a period of high conflict intensity, terrorist population attacks showed both direct and indirect negative effects on the test scores. In 2017, a period of low intensity, only direct negative effects were reported for the variables of forced displaced people, homicides, and victims of threat.