This article examines the Protestant minority’s struggle for freedom of conscious in France from 1789 to 1905, in three steps: The first highlights the role of the pastor Rabaut Saint-Étienne in the proclamation of the freedom of conscience in 1789, with Article 10 of the Declaration of the Rights of Man and of the Citizen. Despite his efforts, the formulation of this principle remained ambiguous, revealing a tension between the recognition of religious freedom and a uniformizing conception of national unity. The second step provides a panoramic overview of the nineteenth century, where Lutheran and Reformed Protestantism were identified as “recognized religions” alongside Catholicism and Judaism. Nevertheless, great struggles on various levels still had to take place before this freedom of conscience became effective, as Catholicism sought to identify itself with the nation and viewed the efforts to rebuild Protestantism as a “threat”. What is more, a part of Protestantism still experienced little more than mere toleration. A third step examines the role played by Protestants in the establishment of secularism through the secularization of public schools (1882) as well as the law for the separation of church and state (1905). With this law, freedom of conscience became the rule, while–with a view to public interest– restrictions formed the exception. Each step raises critical for questions for today. The article thus closes by advocating a dialectical tension between freedom, tolerance, and truth.