In 1872 the French Reformed churches were allowed to convoke an official general synod, the first since the Revocation, not counting those of the Désert. It resulted in two groups: the first adopted the Confession of Faith (by vote in 1872) and an unofficial presbyterian-synodal form of church government (starting in 1879), the other remained presbyterian. The situation would remain that way until the Séparation of 1905. Was this unique in Protestant Europe? No, since the institutionalization of these synods exposes five underlying dilemmas common to most churches: the specific place to be granted to the pastors; the challenge of uniformizing rituals; the adoption of bureaucratic procedures; a theological reformulation of the doctrine of atonement; and the partisan polarization on the issues of the place of religion in the French nation. On the whole, the churches’ organizational form (presbyterian, congregationalist, episcopalian) was as important as their status between pluralism and confessional adherence. The five great variables must therefore be given significant attention for situating the underlying or active governmental politics as well as the spiritual forces in reevaluating the role played by the schisms, which may have been overestimated. It has therefore been suggested that future reflection ought to be carried out in terms of ecclesiasticity regimes so as to reconsider especially the church-sect-mysticism typology developed by Ernst Troeltsch in 1912, which remains stimulating. The interactions between these forms serve to organize the fourteen articles in this special issue.