Abstract Introduction There is a scarcity of research with high quality methods on the effectiveness of mindfulness-based interventions (MBIs) on adolescents’ mental well-being. This study investigates the MBI effects on adolescents’ stress and self-kindness with an extensive cluster RCT design, and a role of self-kindness as a mediator for the association between the MBI and stress. Additionally, the study explores how age, gender, and an independent mindfulness practice moderate the effects on the outcomes. Methods Participants (Finnish students, aged 12-15 years) were randomized to a MBI group (N = 1646), an active relaxation control group (N = 1488), and an inactive control group (N = 385). The outcomes were measured at the baseline (T0), at 9-week post-intervention (T9), and at 26-weeks follow-up (T26). Results Overall, the MBI was more effective in stress reduction when compared to the active control at T9 (β = -0.04, p < 0.01, d = -0.11) and T26 (β = -0.04, p = 0.02, d = -0.11). Furthermore, students in the MBI group who carried out their regular mindfulness home practice showed greater decrease of stress. There were no MBI effects on self-kindness, nor did a change of self-kindness mediate the effects of MBI on stress. Discussion These findings demonstrate that the 9-week MBI is slightly more effective to reduce stress relative to relaxation training. Key messages • The result highlight the potential of MBI in increasing the stress management among students in school context. • To ensure the effectiveness of MBIs in school context we need to teach these skills to teacher students already during their basic education in educational institutions and universities.