Background Stress among students is on the rise during early medical school and has been implicated in poor academic performance. Several methods are being discussed to efficiently reduce stress, among them mindfulness-based interventions. We therefore set out to assess how stress, mindfulness, and academic performance are connected and if an intervention on mindfulness based stress reduction could alleviate stress among medical students and improve their academic achievements. Methods A non-randomized controlled trial including 143 medical students in their preclinical years was performed in 2019. The students completed two surveys - one in the first, the other in the third term - recording perceived stress and mindfulness via validated scales (PSS-10 and MAAS). In between both, 41 students participated in a voluntary mindfulness-based intervention including six two-hours courses. 86 students served as controls. Scholarly success was assessed via the scores achieved in six exams written during the observation period. Results Stress was inversely related with mindfulness and with the results of the most challenging exam. The intervention on mindfulness based stress reduction helped to contain stress and maintain mindfulness during the observation period and this effect lasted for at least six months beyond completion of the intervention. In contrast, beneficial effects on scholarly success were transient and only detectable at completion of the intervention. Conclusion Our observation of short- and intermediate term effects resulting from six individual interventions on mindfulness based stress reduction is encouraging and calls for alternative strategies to induce long-lasting impacts.