With the main goal of identifying the process factors associated with school effectiveness in secondary education, this work presents an innovative methodological proposal. Based on secondary data from the Spanish sample of PISA 2015, high-and low-effectiveness schools were selected by analysing the residuals of the school level (level 2) in multilevel models. Subsequently, decision trees were used to identify the process variables with a greater predictive power for the identification of high-and low-effectiveness schools. While the hierarchical linear models obtained show inter-school variance scores greater than 10%, decision trees achieve a precision greater than 90%. We conclude by analysing the suitability of using decision trees in data originating from large-scale assessments, and examining the obtained factors associated with school effectiveness.