Objective: There is little knowledge about which types of meditation-based training are effective for alleviating which facets of psychological distress. We investigated shared and specific effects of three meditation-based training programs on distress. Method: 332 healthy adults were assigned to a retest control cohort or to one of three 3-month mental training cohorts including: the cultivation of mindfulness-based attention (Presence), socio-affective skills such as compassion (Affect), or metacognitive skills such as perspective taking (Perspective). A battery of 68 self-reported distress measures was collected. Data were analyzed using machine learning methods, identifying the cohort allocation based on distress change scores. Results: Supporting only specific and not shared alleviation effects, the classifiers identified significantly above chance Presence from Affect and Affect from Perspective, but they did not identify the training cohorts from the retest cohorts. Conclusions: The classifiers revealed stable module-associated distress change profiles, which could help to precisely choose meditation-based interventions to target individuals’ specific distress patterns.