Startle stimuli evoke lower responses when presented during the early as compared to the late cardiac cycle phase, an effect that has been called ‘cardiac modulation of startle’ (CMS). The CMS effect may be associated with visceral-afferent neural traffic, as it is reduced in individuals with degeneration of afferent autonomic nerves. The aim of this study was to investigate whether the CMS effect is due a modulation of only early, automatic stages of stimulus processing by baro-afferent neural traffic, or if late stages are also affected. We, therefore, investigated early and late components of auditory-evoked potentials (AEPs) to acoustic startle stimuli (105, 100, 95 dB), which were presented during the early (R-wave +230 ms) or the late cardiac cycle phase (R +530 ms) in two studies. In Study 1, participants were requested to ignore (n = 25) or to respond to the stimuli with button-presses (n = 24). In Study 2 (n = 23), participants were asked to rate the intensity of the stimuli. We found lower EMG startle response magnitudes (both studies) and slower pre-motor reaction times in the early as compared to the late cardiac cycle phase (Study 1). We also observed lower N1 negativity (both studies), but higher P2 (Study 1) and P3 positivity (both studies) in response to stimuli presented in the early cardiac cycle phase. This AEP modulation pattern appears to be specific to the CMS effect, suggesting that early stages of startle stimulus processing are attenuated, whereas late stages are enhanced by baro-afferent neural traffic. •It is unclear if the cardiac modulation of startle (CMS) is due to early or late stages of stimulus processing.•We investigated auditory-evoked potentials (AEPs) in response to acoustic startle probes.•N1 amplitudes were lower for startle stimuli presented in the early cardiac cycle phase.•P2 and P3 amplitudes were higher for stimuli presented in the early cardiac cycle phase.•Early stages of startle processing are attenuated, whereas late stages are enhanced by baro-afferent neural feedback.