There is a growing interest in the study of active methodologies, especially cooperative learning. It will allow for skills related to the positive interdependence between the components of a group, individual responsibility, the encouragement of interaction, and the development of social skills to be put into practice by pre-service teachers, as well as for the sharing and assertiveness of the ideas of teamwork. The purpose of this study is to predict those variables that significantly positively affect pre-service teachers’ perceptions about the use of cooperative learning methodology in their initial training at university once it has been put into practice in the classroom for 3 months. For this, a quasi-experimental design was implemented to enable its practice, and subsequently the perceptions of the pre-service teachers were collected through the use of a questionnaire. The sample was composed of 140 pre-service teachers from the Faculty of Education of the University of Almeria (Spain). The overall results of the study determined that the interest of pre-service teachers in their subject, age, attendance of practical classes, and the type of education level they have had access to positively affect the perceptions of pre-service teachers, while positive academic performance causes a decline. These findings highlight the need to continue research, mainly on the question of why working in cooperative groups causes a decrease in academic performance.