BACKGROUND: Antisocial behaviours make social interactions difficult among students. Moral emotions, online empathy, and anger management are social and emotional variables related to prosocial and antisocial behaviours and health problems. This research aims to assess the impact of Cooperative Project-Based Learning intervention on these three variables for Primary Education students. Additionally, the relations of these variables with key competencies, such as social and emotional competencies and literacy competence, were studied. METHOD: This research is made up of two studies, descriptive and quasi-experimental, during regular school hours. The descriptive study was carried out with a sample of 516 primary school students and aimed to assess the development of the three variables, taking into account personal and ethnic-cultural factors. The quasi-experimental study, with pre-test and post-test data, had the participation of 145 students to study the incidence of these variables after Cooperative Project-Based Learning intervention in Primary Education. RESULTS: The results show the relation among the cited variables and the positive impact of the intervention on moral emotions and anger management in the experimental group compared to the control group. Experimental group girls presented higher scores in moral emotions than control group girls. CONCLUSION: These results open new research lines in relation to the intervention as a programme to prevent the appearance of antisocial behaviours and health problems at school.