Meditation training is presumed to influence individuals’ emotional engagement with others’ suffering. Although evidence is accumulating for the prosocial effects of intensive practice in meditation, little is known about how training may alter primary cognitive representations of compassion-eliciting stimuli. We assessed individuals’ remote (six-year) incidental memory for emotional images viewed both before and after a three-month intensive shamatha retreat. Physiological patterns at initial stimulus encoding suggest that training may selectively enhance negative affect (potentiated startle) and stimulus orienting (cardiac deceleration) to suffering-related, but not fear-related, stimuli. At retrieval, participants were able to differentiate old from new images more than six years after initial exposure, and they showed preferential remembering of suffering-related stimuli, as assessed via speeded response. We suggest that intensive meditation training strengthens motive system responses to depictions of suffering, leading to extended and elaborated processing, as evident in memory retention over very long intervals.