Following the judgment with roughing-hew of Michel Servet, and to refute the treaty in favor of the tolerance of Sebastien Castellion, Bèze published into 1554 Of haeriticis has civili magistratu puniendis, whose French translation will appear in 1560 pennies the Traité title of the authority of the magistrate in the punishment of the heretics, more known under the name of Traité of the heretics; Bèze shows there a partisan of the most extreme punishments against the heretics, the punishments not being able in any event to correspond “to the hugeness of such a fixed price”.  

In 1558, it left Lausanne and settled in Geneva where it found a station with the Academy; he then became the principal collaborator of Calvin. In August 1561, it represented the calvinists at the time of the oecumenical conference joined together in Poissy, on the authorities of the Michel chancellor of Hospital, which hoped to manage an agreement between roman catholics and reformed; of Bèze, by affirming its refusal so much transsubstantiation (catholic) that consubstantiation (Lutheran), ruined the hopes of the chancellor. He did not return however immediately to Geneva, and Catherine de Médicis, who wanted to still accept a possible agreement, retained it some time near her, the consultant on her decisions of religious policy.  

In 1564, the death of Calvin, Bèze succeeded to him in the loads which it occupied in Geneva. In 1574, it published right of the magistrates on their subjects; it develops the idea to with it that the goal of the State is to work with the happiness of the subjects, and that, out of religious matter, the civil power must be put at the service of the Church and repress the heresies.  

One owes him a tragedy, Abraham sacrificing (1550), and of many works in religious matter: Psalms (1553-1563), Life of Calvin (1563), Course on the epistles with the Romans and the Hebrews (1564-1566), True Portraits of the famous men (1573), ecclesiastical History of the reformed Churches of the kingdom of France (1580). Moreover, its correspondence, very bulky, was preserved and published.