Geneva’s Protestants were divided during successive crises throughout the nineteenth century, over beliefs as well as institutional organization, the role of the clergy, and the church’s place in society. This article analyzes each of the phases of these schisms – the Awakening, the creation of the Free Churches, and the division between evangelicals and liberals – by pointing out, in their context, the underlying issues. The main conflicts concern the heritage of Calvin and his theology, the clash between biblical tradition and rationalism, and the supervision of the faithful. In all these cases, the core of the problem lies in Protestantism’s handling of modern individual rights: should democracy and religious freedom be integrated in ecclesiology and pastoral care, i.e., take place within the church itself? Two opposing models of the Protestant community were at stake: a confessional (evangelical) model, and a model of the community as embracing the entire Geneva population. This fracture was one factor leading the canton of Geneva towards the separation of the church and state in 1907.