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This paper refers to whole school interventions aiming to promote student learning outcomes through improving the functioning of school factors. Evaluation studies of these interventions mainly measure their impact on student learning outcomes. This paper argues for the importance of studying the mechanisms of whole school interventions through testing the theoretical framework upon which each intervention is based. We stress the importance of using Multilevel Structural Equation Model (MSEM) for identifying indirect effects of whole school interventions on student learning. To illustrate the strengths of this approach, we present an experimental study investigating the impact of the Dynamic Approach to School Improvement (DASI) on promoting student learning outcomes. The methods of this study and the use of mediation MSEM in a 2-2-1 design to test the main theoretical assumption of DASI are presented. The intervention was found to have both a direct (d = 0.21) and an indirect effect (d = 0.13) on student achievement in mathematics. Implications for designing and evaluating theory-driven school improvement approaches are drawn.