This chapter analyzes the collective dimension of freedom of religion under the European Convention on Human Rights, arguing that individual religious liberty is ineffective unless religious communities can organize and function autonomously. Drawing on Strasbourg jurisprudence, it shows how Article 9 must be read in light of Article 11 to protect the associative life of religious groups and to preserve pluralism in democratic society. The chapter identifies two foundational principles structuring the Court’s approach: autonomy and state neutrality. It examines the Court’s protection of internal self-governance while also highlighting persistent tensions between institutional autonomy and individual rights in fields such as employment, education, and internal dissent, including the emergence of “ministerial exception”-type reasoning. The chapter then explores neutrality as a requirement of impartiality and procedural fairness in state regulation of religion, focusing on registration, legal personality, and access to privileges. It concludes that while autonomy and neutrality operate as essential safeguards for religious pluralism, their practical effectiveness is shaped by broad margins of appreciation and uneven scrutiny, which can entrench structural disadvantages for minority faiths.