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This study of the use of metacognitive strategies during learning interaction in collaborative groups is considered referential for understanding the development of such strategies. The use of metacognitive strategies is related to better learning outcomes. We monitored the interaction in five collaborative groups at three points in time (initial, intermediate and final). These groups consisted of undergraduate health science (n = 9) and biomedical engineering students (n = 10). The aims were the following: (1) To check whether there were significant differences in the use of metacognitive strategies between the groups of students monitored depending on the type of degree or the point in time measurement. (2) To test whether there were significant differences in students’ learning outcomes depending on whether or not they had participated in the interaction monitoring during collaborative interaction. (3) To test clustering without a pre-assignment variable against learning outcomes in collaborative groups. Significant differences were detected in the use of some of the metacognitive strategies of orientation, planning and elaboration in favor of the collaborative groups of the biomedical engineering students. Also, students who participated in monitoring collaborative groups in both clusters obtained better learning outcomes. Lastly, the assignment groups were exactly related to the collaboration groups with respect to the use of metacognitive strategies in the final measurement.