First, based on self-categorization theory, we conceptualize multilevel forms of collective identity, namely embedded and dis-embedded identity. These describe different forms of the identification with one’s religious community and one’s society as well as the perception of the (dis-)embeddedness of one’s community within or from one’s society. For the purpose of validation, we analyze data from five cross-sectional samples of religious communities within different societies. The data provide support for our conceptualizations. Second, we examine the predictive value of embedded and dis-embedded identity for (in)tolerance of religious groups toward disapproved outgroups such as atheists, feminists, homosexuals, or Muslims. Based on self-categorization theory and the disapproval–respect model of tolerance, we deduce the conceptual match between (dis-)embedded identity and (in)tolerance. Also, tolerance is proposed as the reasonable response to intergroup conflicts. We hypothesize embedded identity to positively predict but dis-embedded identity to negatively predict tolerance. Data from three longitudinal samples of religious communities within different societies are analyzed. The results provide partial support for the positive relation between embedded identity and tolerance but consistent support for the negative relation between dis-embedded identity and tolerance. The implications for tolerance of and for religious communities in modern societies are discussed.