The European Court of Human Rights recognizes a right of religious organizations to autonomy, both doctrinal and disciplinary. It set this principle aside in the case of Tothpal and Szabo v. Romania of 19 February 2019, in favour of a more individualistic vision of religious freedom. This stance is surprising, but will probably remain isolated in the Court’s case law. Beyond this point, the article offers a reflection on the difficult implementing of the duty of neutrality of the State in religious matters. It highlights some theological presuppositions implicitly entailed in the Court’s argument and questions their religious neutrality.