The goal of the article was to compare the effects of two different cooperative learning programmes on prospective teachers. A total of 332 students enrolled in a Teacher Training Programme agreed to participate. At the beginning of the semester, they all experienced low-structured cooperative learning (LSCL) for 10 sessions. At the end of this phase (T1), research variables were assessed and the groups were randomly divided into two different conditions for 10 new sessions: high-structured cooperative learning (HSCL) and LSCL. At the end of this period, research variables were assessed again (T2). Results at T2 showed that only participants in the HSCL group significantly increased their motivation, content knowledge, responsibility and the five elements that mediate Cooperative Learning effectiveness: positive interdependence, individual accountability, promotive interaction, group processing, and social skills. There was also a significant increase in shared-regulation dominance. In conclusion, cooperative learning can have a positive impact on prospective teachers' academic performance, but it needs to be highly structured.