The subjective construction surrounding the perception of negative experiences is partly built upon bodily afferent information, comprising heart, gut or respiratory signals. While this bottom-up influence has been extensively described, the opposite pathway, the putative influence of cognitive processes over autonomic response, is still debatable. Emotion regulation and the ability to control maladjusted physiological response associated with thoughts and memories is a recurrent concern for most psychiatric disorders and mental health as a whole. Memory suppression (i.e. exerting inhibitory control toward unwanted memories) has been proposed as a possible solution to perform such regulation. This method, however, also holds debates as it could putatively worsen distressing reactions when unsuccessful, or simply be ineffective on the physiological roots of emotions. Here, we tested the hypothesis that memory suppression can influence the physiological marker of emotions in two studies using the "Think/No-Think" paradigm. We measured in healthy participants the aftereffect of suppressing negative memories on their cardiac reaction toward the excluded memories. Results of Study 1 revealed that an efficient control of memories was associated with a long-term inhibition of the cardiac deceleration normally induced by disgusting stimuli. Attempts to suppressing sad memories, on the opposite, aggravated cardiac response, an effect that was largely related to the inability to forget this specific material. Study 2 recorded concurrent electroencephalographic (EEG) response during the TNT task to track the oscillatory dynamics supporting the inhibitory control of memories and estimate their role in the inhibition of the later cardiac response. We found that the decrease of the 5-9 Hz frequency band, a prominent electrophysiological marker of memory suppression, was indeed related to the subsequent inhibition of the cardiac response toward disgusting stimuli. These results show that the modulation of cognitive representations can have long-term effects on the cardiac system. They further support the notion that cognitive control over unwanted emotional memories, when successful, can reduce the autonomic aversive processes to achieve emotional regulation. Our findings open new avenues for possible interventions focused on training this suppression mechanism to reduce the impact of distressing intrusive memories on mental health.