Affective polarization, the growing emotional distance between identity-based groups, has become a pressing issue in recent years. Prior research has shown that mutual dislike and out-group hostility lead to moral disengagement, discrimination and even (support for) political violence. However, the specific mechanisms that underly those negative outcomes are less clear. This study aims to address this gap by examining the relationship between affective polarization and political intolerance, understood as the denial of civil liberties by opposing political groups. After all, since mutual dislike and emotional distance are known to erode democratic norms, this paper advances the literature on affective polarization by further exploring how emotional conflict within identity-based groups might lessen the support for civil liberties for one’s political opponents. Drawing on a novel survey of UK citizens (n = 1000) that uses detailed measures of polarization on topics such as Brexit, transgender rights, and political orientation, this research sheds light on how affective polarization drives political intolerance.