Can secessionism be a basis for affective or social polarization? Despite much research on independence movements, their relationship to polarization, a key mechanism theorized as increasing the risk of violent conflict, remains less understood. We argue that the issue of secession can affectively polarize along both policy and ethnic group lines even in the case of nonviolent disputes, and posit a number of expectations regarding such secessionist-based polarization. We test our argument with the case of Catalonia, a substate territory that has experienced a deep secessionist crisis since 2017, using new data from a panel survey and embedded experiments fielded across two key time periods. We find that individuals’ secessionist preferences condition high levels of affective polarization, in that pro- and anti-independence advocates have strong negative views of one another. In addition, there is spillover in terms of stereotypes of associated language groups (i.e. Catalan, Spanish). Importantly, we find a group of moderates in between the two policy poles that exhibit far less polarization. Finally, we document the persistence of these overall patterns. Our results contribute to understanding the underexplored polarization dynamics of secessionist movements, particularly in contexts where high intensity violence (e.g. terrorism, civil war) has not occurred.