Adapting to the ever-changing demands of the environment requires a complex interplay between cognitive-affective, neuronal, and autonomic processes. Vagally-mediated heart rate variability (vmHRV) is positively associated with both cognitive-affective functioning and prefrontal cortex (PFC) activity. Accordingly, the Neurovisceral Integration Model has posited a shared role of the PFC in the regulation of cognitive-affective processes and autonomic nervous system (ANS) activity. While there are numerous correlational findings in this regard, no study so far has investigated whether the manipulation of PFC activity induces changes in vmHRV and cognitive-affective processing in an inter-dependent manner. In this study, we examined the effects of continuous (cTBS) and intermittent theta-burst stimulation (iTBS) over the left dorsolateral PFC (dlPFC) on vmHRV and cognitive-affective processing within an emotional stop-signal task (ESST) in 66 participants. Our results revealed that both resting vmHRV and reactivity, at least partly, predicted cognitive-affective processing. Furthermore, we found a dampening effect of cTBS on resting vmHRV, as well as an enhancing effect of iTBS on ESST performance. Our results show no direct association between vmHRV changes and ESST performance alterations following stimulation. We interpret our results in the light of a hierarchical model of neurovisceral integration, suggesting a dynamical situation-dependent recruitment of higher-order cortical areas like the dlPFC in the regulation of the ANS. In conclusion, our results highlight the complex interplay between PFC activity, autonomic regulation, and cognitive-affective processing, emphasizing the need for further research to understand the causal dynamics of the underlying neural mechanisms.