In educational contexts, certain issues are perceived as controversial, since they reflect conflicts of interest and reveal divergent views. This is especially evident in debates related to religion in societies regarding themselves as secular but whose population is multi-religious. The aim of this article is to analyse how some issues that are considered controversial in the public debate are represented in the teaching of non-denominational and integrative Religious Education in a Swedish multicultural classroom practice, where the majority of students have a Muslim cultural background. The ethnographic empirical material consists of classroom observations of Religious Education lessons in upper secondary school. The analysis is based on the debate about how controversial issues ought to be taught—as empirically or politically open/settled or in a directive/non-directive way. The results indicate that a number of issues—divergent interpretations of religious narratives and religiously motivated rules, holidays, views of forgiveness, the Israeli–Palestinian conflict and abortion—were regarded as open political issues in classroom practice and these were taught in an open, non-directive way. Issues represented as settled were value-oriented issues related to female genital mutilation, forced marriage and child marriage and gender equality. The arguments supporting these values were mainly rooted in religion. © 2020 by the author. Licensee MDPI, Basel, Switzerland.