The dropout rate of university engineering studies is correlated with the absence of retention of freshman in the basic subjects. The aim of this work is to determine the effect of cooperative learning and the characteristics of students on learning, persistence, and academic performance. We have performed a study of learning, persistence and academic performance in an engineering physics course, comparing two groups with different teaching, one traditional and the other through cooperative learning. In addition, we have analysed the influence of the characteristics of the students on the results and the perceptions of the students regarding the teaching. The students of the cooperative learning group had a normalised average gain in the Force Concept Inventory that was 72.7% higher, a significantly higher persistence, and a final grade similar to that of the group receiving traditional teaching. The previous education and the size of the community of origin of the students had a significant effect on the persistence of the students. The perceptions of the subject and lecturer were similar in both groups.