This study examines church–state relations in Europe, and analyzes their influence on anti‐immigrant attitudes. The literature explains this relationship primarily with religious demographics, or state privileges for the majority faith. Alternately, this study focuses on the status of the majority religion. It argues that, in countries with a national church, citizens are more likely to consider the institutionalization of a new religion to be occurring at the expense of the national heritage, and react negatively. To test that hypothesis, the study focuses on Muslim immigrants in Europe, and builds an index that gauges the extent to which European states institutionalize Islam. Then, employing multilevel regression analysis, it investigates how the institutionalization of Islam influences anti‐Muslim prejudice in different contexts of church–state regimes. Individual‐level data come from the latest wave of the European Values Study, and cover 31 countries. Findings indicate that, in European countries with a national church, institutionalization of Islam increases anti‐Muslim prejudice. In countries without a national church, however, institutionalization leads to tolerance. These results confirm the continuing relevance of religion on the national level in Europe, despite the decline in individual religiosity.