Background: Teaching methods that stimulate the active learning of students make a positive impact on several aspects of learning in higher education. Collaborative testing blended with teaching is one such method. At our medical school, a training session was designed using a collaborative testing format to engage medical students actively in the theoretical phase of a physical examination training, and this session was evaluated positively by our students. Therefore, we extended the use of the format and converted more of the training into collaborative testing sessions. The literature on collaborative testing and the theoretical framework underlying its motivational mechanisms is scarce; however, students have reported greater motivation. The aim of the current study was to investigate student perceptions of a collaborative testing format versus a traditional teaching format and their effects on student motivation. Methods: Year four medical students attended seven physical examination training sessions, of which three followed a collaborative testing format and four a traditional format. The students were asked to evaluate both formats through questionnaires comprised of two items that were answered on a five-point Likert scale and five open-ended essay questions. Content analysis was conducted on the qualitative data. The themes from this analysis were finalized through the consensus of the full research team. Results: The quantitative data showed that 59 students (55%) preferred collaborative testing (agreed or strongly agreed), 40 students (37%) were neutral, and 8 students (8%) did not prefer collaborative testing (disagreed or strongly disagreed). The themes found for the collaborative testing format were: ‘interaction’, ‘thinking for themselves’, and ‘active participation’. ‘Interaction’ and ‘thinking for themselves’ were mainly evaluated positively by the students. The most frequently mentioned theme for the traditional format was: ‘the teacher explaining’. Students evaluated this theme both positively and negatively. Conclusions: The most frequently mentioned themes for the collaborative testing format, namely ‘interaction’, ‘thinking for themselves’, and ‘active participation’, fit within the framework of self-determination theory (SDT). Therefore, the collaborative testing format may support the fulfilment of the three basic psychological needs indicated in SDT: autonomy, competence, and relatedness. Thus, our findings provide initial support for the idea that the use of collaborative testing in medical education can foster the autonomous motivation of students.