During the last decades, a significant increase in empirical studies concerning school violence is observed. Evidence-based interventions that promote positive school climate have been found to improve social competence, resilience, and students' well-being in schools, resulting in team bonding, feelings of acceptance, respect, and a sense of belonging. The present study explores junior high school students' perceptions regarding school climate dimensions referring to safety and relationships (i.e., discipline/order, positive peer relations, bullying prevention, respect of diversity). The sample consisted of 726 students from junior high schools in the broader area of Athens (mean age 14.4 years). Questionnaires regarding school climate dimensions focusing on safety and relationships, subjective well-being, economic crisis difficulties, and demographic data including gender, school grade, and academic performance were completed. Using conditional process analyses, the effect of a three-way interaction between school climate, academic performance, and economic difficulties on junior high school students' subjective well-being is examined. Gender and school grade are also studied. Results suggest that positive peer relations, bullying prevention, and respect for diversity associated with academic performance (but not with gender and school grade) moderate the relationship between economic difficulties and subjective well-being. The development and implementation of several intervention programs in diverse school settings in the Greek educational system are briefly discussed focusing on their effectiveness and usefulness regarding the promotion of school well-being and prevention of bullying and school violence.