We present results from a large-scale study performed in Flanders, focusing on the effectiveness of the eco-schools project. We surveyed 2152 students and 1374 teachers in 101 primary and secondary schools that are actively engaged in the eco-schools program at different stages (including control schools), focusing on their environmental values, knowledge and motivation. The results show that as the schools progress in becoming a certified eco-school, their students' environmental outcomes change; the eco-schools project thus clearly has an educational impact. The main effects are observed for theoretical knowledge, and to a lesser extent, applied knowledge. We also observed a drop in utilization values and in amotivation. On the other hand, the controlled motivation of students is stimulated by the project as it is implemented, suggesting that students act pro-environmentally due to external pressures rather than because of intrinsic reasons. We also explicitly moved beyond comparing schools based on their eco-schools labels and studied the process factors that contribute to learning outcomes. Our results highlight the importance of the approach to didactics for environmental education, the making of environmental education policy in the schools, and the presence and use of natural green elements at the school campuses. For each of these school-level variables, the impact on students' environmental learning outcomes are studied and discussed.