Meditation-based mental training interventions show physical and mental health benefits. However, it remains unclear how different types of mental practice affect emotion processing at both the neuronal and the behavioural level. In the context of the ReSource project, 332 participants underwent an fMRI scan while performing an emotion anticipation task before and after three 3-month training modules cultivating 1) attention and interoceptive awareness (Presence); 2) socio-affective skills, such as compassion (Affect); 3) socio-cognitive skills, such as theory of mind (Perspective). Only the Affect module led to a significant reduction of experienced negative affect when processing images depicting human suffering. In addition, after the Affect module, participants showed significant increased activation in the right supramarginal gyrus when confronted with negative stimuli. We conclude that socio-affective, but not attention- or meta-cognitive based mental training is specifically effective to improve emotion regulation capabilities when facing adversity.