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Stress may affect cardio-afferent neural traffic. We investigated whether acute autonomic stress has an impact on cardiac modulation of startle (CMS), a ‘background’ methodology for assessing baro-afferent signal transmission. Therefore, 38 healthy volunteers received acoustic startle stimuli (105 dB) at 6 different latencies relative to the R-wave (R + 0, 100, 200, 300, 400, and 500 ms; randomized order), both before and immediately after either a cold pressor (n = 19) or a control intervention (n = 19). Blood pressure was enhanced significantly in the cold pressor group right after the intervention (+ 13.7/5.7 mm Hg), reflecting sustained autonomic activation after the stress procedure. Before stress, startle responses were lowest for latencies of R + 200 and + 300 ms, corroborating previous findings. After the cold pressor test, startle responsiveness was lowest for earlier latencies (R + 0, + 100 and + 200 ms). Stress facilitation of pre-ejection baro-afferent traffic originating from atrial mechano-sensitive receptors may be associated with this time shift effect. We conclude that the cardiac modulation of startle is sensitive to altered temporal baro-afferent feedback characteristics induced by stress and autonomic activation.