Previous studies support the relevance of students’ perception of positive and negative school climate to learning processes and adolescents’ adjustment. School climate is affected by both the interactions that are established within the classroom, and by the teachers’ behaviors. This study has the overall objective of investigating the relationship between the perception of positive and negative school climate and students’ (mal)adjustment during adolescence. Participants were 105 Italian adolescents (52.5% boys, mean age = 15.56,SD = .77) who responded for 15 consecutive days (ecological momentary assessment) to questions related to their perception of positive and negative school climate (Time 1). After one year (Time 2), students’ academic performance reported by mothers and fathers and adolescents’ self-reported propensity to engage in risk behaviors were examined. Four hierarchical regression models were implemented considering the mean and the instability levels (RMSSD) of the perception of positive and negative school climate as independent variables and, respectively, academic performance and risk behaviors as dependent variables. Results suggest that a higher perception of positive school climate and its instability predict higher academic performance one year later, while a higher perception of negative school climate and its instability predict higher risk behaviors. This study provides an innovative perspective to reflect on the relationship between students’ perceptions of school climate and adolescents’ (mal)adjustment.