Increases in cultural and religious diversity have led to calls for toleration of differences, although it is unclear how calling for toleration impacts people’s affective and attitudinal responses. The present research conducted in a small western nation examines if calling for toleration of Muslim minority practices elicits an aggressive backlash against the group amongst those relatively conservative, using relative left frontal EEG activity to examine the motivational processes involved. Non-Muslim participants from New Zealand (N = 172) self-reported their political orientation before being randomly assigned to a toleration or control condition involving writing and reflection tasks about Muslims. Participants then evaluated various groups including Muslims while EEG was recorded. Results revealed that among those relatively conservative, toleration produced higher levels of relative left frontal activity, which in turn led to more negative evaluations of Muslims (relative to control participants). However, for those relatively liberals, toleration had no impact on neuropsychological or attitudinal responses relative to controls. Collectively, these findings suggest that intergroup toleration may backfire amongst those relatively conservative, undermining its intended purpose.