Introduction: The problem of school violence has been studied in the last decades from different perspectives, especially focused on bullying conflicts. Whole school approaches have been recommended by many experts in the field. The aim of the present study is to assess climate changes in two secondary schools that implement a peer support program, and to understand the level of perceived satisfaction. Method: Pre-post study with experimental and control group. Participants were 778 pupils (3 phases) plus 65 teachers at the experimental school; 462 pupils and 29 teachers at the control school. The tools used were questionnaires, focus groups and intensive interviews. Results: All participants believe that the peer support program is useful for improving the perception of safety at school, while the responses of the control school students indicate a general increase in the frequency of conflicts. Discussion and Conclusion: Results show the complexity of controlling all the variables linked to changes of context. However, as proposed previously by other authors, objective measures need to used in assessing school climate, in addition to perceptions shown on self-reports, in order to accurately determine the impact of peer support programs.