Emotional dysregulation is a transdiagnostic factor underlying various psychopathologies. Mindfulness may effectively reduce distress and enhance psychological well-being by positively influencing emotional regulation processes, including self-compassion. This study investigates the effect of mindfulness-based stress reduction (MBSR) training on mindfulness skills, self-compassion, and the incidence of emotional dysregulation. It also evaluates self-compassion's moderating effect on emotional dysregulation. Seventy-nine participants completed the MBSR protocol. They filled out the Five Facet Mindfulness Questionnaire (FFMQ) for mindfulness skills, the Self-Compassion Scale (SCS) for self-compassion, and the Difficulties in Emotion Regulation Scale (DERS) for emotional dysregulation, both before and after MBSR training. Mixed model analyses showed a significant increase in mindfulness skills (FFMQ), a reduction in emotional dysregulation (DERS), and a significant increase in self-compassion (SCS) from pre-to post-MBSR (all p ≤ 0.001). Emotional dysregulation incidence decreased (χ2 = 8.59; p = 0.003). Multinomial logistic regression revealed that lower mindfulness (β = 0.86; p = 0.020) and a smaller increase in the sense of shared humanity (SCS; β =-1.78; p = 0.046) modulated MBSR’s effect. These findings support MBSR's positive impact on emotional regulation, suggesting it may benefit transdiagnostic risk factors in various psychopathologies.