Morally challenging decisions tend to be perceived as difficult by decision makers and often lead to post-decisional worry or regret. To test potential causes of these consequences, we employed realistic, morally challenging scenarios with two conflicting choice options. In addition to respondents’ choices, we collected various ratings of choice options, decision-modes employed, as well as physiological arousal, assessed via skin conductance. Not surprisingly, option ratings predicted choice, such that the more positively rated option was chosen. However, respondents’ self-reported decision modes also independently predicted choice. We further found that simultaneously engaging in decision modes that predict opposing choices increased decision difficulty and post-decision worry. In some cases this was related to increased arousal. Results suggest that at least a portion of the negative consequences associated with morally challenging decisions can be attributed to conflict in the decision modes one engages in.