Previous research suggests that implicit automatic emotion regulation relies on the medial prefrontal cortex (mPFC). However, most of the human studies supporting this hypothesis have been correlational in nature. In the current study, we examine how changes in mPFC-left amygdala functional connectivity relate to emotional memory biases. In a randomized clinical trial examining the effects of heart rate variability (HRV) biofeedback on brain mechanisms of emotion regulation, we randomly assigned participants to increase or decrease heart rate oscillations while receiving biofeedback. After several weeks of daily biofeedback sessions, younger and older participants completed an emotional picture memory task involving encoding, recall, and recognition phases as an additional measure in this clinical trial. Participants assigned to increase HRV (Osc+) (n= 84) showed a relatively higher rate of false alarms for positive than negative images than participants assigned to decrease HRV (Osc−) (n= 81). Osc+ participants also recalled relatively more positive compared with negative items than Osc− participants, but this difference was not significant. However, a summary bias score reflecting positive emotional memory bias across recall and recognition was significantly higher in the Osc+ than Osc− condition. As previously reported, the Osc+ manipulation increased left amygdala-mPFC resting-state functional connectivity significantly more than the Osc− manipulation. This increased functional connectivity significantly mediated the effects of the Osc+ condition on emotional bias. These findings suggest that, by increasing mPFC coordination of emotion-related circuits, daily practice increasing heart rate oscillations can increase implicit emotion regulation.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10484-023-09579-1.