Although much has been written about the beneficial effects of the Jigsaw method, little is known about how it affects students' motivation and self-regulation processes. In this study, we tested its effects on students' trajectories of autonomous mathematics motivation and academic self-regulation. We also examined whether these effects could be moderated by the students’ cooperative attitudes and initial mathematics achievement level. 4,698 students from French vocational high schools participated in the study over two years. They were divided into three groups: 1,641 were assigned to a cooperative learning condition with the Jigsaw method, 1,602 to a weakly structured cooperative learning condition, and 1,455 to a business-as-usual learning condition. Self-reported mathematics motivation, academic self-regulation, and cooperative attitudes were collected three times during the study. Overall, the multilevel growth model results indicate a general decline in students’ motivation and self-regulation, and student-reported cooperative attitudes did not moderate these effects. However, the trajectories of motivation and self-regulation differed by condition for low-achieving students. While these trajectories decreased over time amongst low-achieving students in the Jigsaw method condition and in the weakly structured cooperation condition, they were stable in the business-as-usual learning condition. These results provide a new perspective since they seem to question the implementation conditions of the Jigsaw method for low-achieving students.