In recent decades, efforts have been made to achieve a positive coexistence among adolescents in secondary schools and create a healthy environment to prepare them to face the present-day challenges. Therefore, this study highlights the educational purpose of improving emotional management and social skills as well as decreasing antisocial and criminal behaviour among secondary education students through an educational training programme. Accordingly, to verify the effectiveness of the project, a quasi-experimental design with a pre-test/post-test structure and a control group was adopted. To achieve this, a total of 141 Spanish secondary school students participated in this study and were randomly assigned to one of two experimental conditions. The first (experimental) group (n = 55) participated in the training programme; correspondingly, the second group (control) (n = 57) followed the usual mentoring activities planned for the entire educational centre. Of the total number of participants, 52.7% of the sample were men and 47.3% were women. The mean age of the participants was 13.01 years old (SD = 0.935). The results showed improvements in the environment with adequate training and the correct application of a programme involving emotional intelligence (EI) among secondary education students. Furthermore, a decrease in conflicts and enhanced relations between the members of the educational community was evidenced. Finally, the practical implications for improving coexistence in secondary schools are discussed.