In three experiments, we explore the link between peripheral physiological arousal and logicality in a deductive reasoning task. Previous research has shown that participants are less likely to provide normatively correct responses when reasoning about emotional compared to neutral contents. Which component of emotion is primarily involved in this effect has not yet been explored. We manipulated the emotional value of the reasoning stimuli through classical conditioning (Experiment 1), with simultaneous presentation of negative/neutral pictures (Experiment 2), or by using intrinsically negative/neutral words (Experiment 3). We measured skin conductance (SC) and subjective affective ratings of the stimuli. In all experiments, we observed a negative relationship between SC and logicality. Participants who showed greater SC reactivity to negative stimuli compared to neutral stimuli were more likely to make logical errors on negative, compared to neutral reasoning contents. There was no such link between affective ratings of the stimuli and the effect of emotion on reasoning.