We investigated the short- and long-term effects of two different evidence-based mindfulness training on students' stress and well-being. A randomised controlled trial with three measurement points (baseline, post-intervention, and 4 months post-intervention) was conducted among undergraduate students of medicine, dentistry, psychology, and logopaedics at the University of Helsinki. The participants were randomly assigned into three groups: (1) face-to-face mindfulness training based on the Mindfulness Skills for Students course (n = 40), (2) a web-based Student Compass program using Mindfulness and Acceptance and Commitment therapy (n = 22), and (3) a control group that received mental health support as usual (n = 40). The primary outcome was psychological distress measured using the Clinical Outcomes in Routine Evaluation Outcome Measure (CORE-OM). Secondary outcomes included hair cortisol concentrations and a wide range of well-being indicators. Psychological distress increased in all the groups from baseline to post-intervention, but significantly less so in the intervention groups than in the control group. At 4-month follow-up, were found no differences between the primary outcomes of the control and intervention groups, but the participants who continued practising mindfulness at least twice a week were less stressed than the others. Our results suggest that participating in a mindfulness course may mitigate health care students' psychological distress during the academic year, but only if the participants continue practising mindfulness at least twice a week.