structural:scholar_edition, quality:corruption
Reform in Geneva (1541–1549)

In supporting Calvin's proposals for reforms, the council of Geneva passed the Ordonnances ecclésiastiques (Ecclesiastical Ordinances) on 20 November 1541. The ordinances defined four orders of ministerial function: pastors to preach and to administer the sacraments; doctors to instruct believers in the faith; elders to provide discipline; and deacons to care for the poor and needy. They also called for the creation of the Consistoire (Consistory), an ecclesiastical court composed of the elders and the ministers. The city government retained the power to summon persons before the court, and the Consistory could judge only ecclesiastical matters having no civil jurisdiction. Originally, the court had the power to mete out sentences, with excommunication as its most severe penalty. The government contested this power and on 19 March 1543 the council decided that all sentencing would be carried out by the government.

In 1542, Calvin adapted a service book used in Strasbourg, publishing La Forme des Prières et Chants Ecclésiastiques (The Form of Prayers and Church Hymns). Calvin recognized the power of music and he intended that it be used to support scripture readings. The original Strasbourg psalter contained twelve psalms by Clément Marot and Calvin added several more hymns of his own composition in the Geneva version. At the end of 1542, Marot became a refugee in Geneva and contributed nineteen more psalms. Louis Bourgeois, also a refugee, lived and taught music in Geneva for sixteen years and Calvin took the opportunity to add his hymns, the most famous being the Old Hundredth.

In the same year of 1542, Calvin published Catéchisme de l'Eglise de Genève (Catechism of the Church of Geneva), which was inspired by Bucer's Kurze Schrifftliche Erklärung of 1534. Calvin had written an earlier catechism during his first stay in Geneva which was largely based on Martin Luther 's Large Catechism. The first version was arranged pedagogically, describing Law, Faith, and Prayer. The 1542 version was rearranged for theological reasons, covering Faith first, then Law and Prayer.

Historians debate the extent to which Geneva was a theocracy. On the one hand, Calvin's theology clearly called for separation between church and state. Other historians have stressed the enormous political power wielded on a daily basis by the clerics.

During his ministry in Geneva, Calvin preached over two thousand sermons. Initially he preached twice on Sunday and three times during the week. This proved to be too heavy a burden and late in 1542 the council allowed him to preach only once on Sunday. In October 1549, he was again required to preach twice on Sundays and, in addition, every weekday of alternate weeks. His sermons lasted more than an hour and he did not use notes. An occasional secretary tried to record his sermons, but very little of his preaching was preserved before 1549. In that year, professional scribe Denis Raguenier, who had learned or developed a system of shorthand, was assigned to record all of Calvin's sermons. An analysis of his sermons by T. H. L. Parker suggests that Calvin was a consistent preacher and his style changed very little over the years. John Calvin was also known for his thorough manner of working his way through the Bible in consecutive sermons. From March 1555 to July 1556, Calvin delivered two hundred sermons on Deuteronomy.

Voltaire wrote about Calvin, Luther and Zwingli, "If they condemned celibacy in the priests, and opened the gates of the convents, it was only to turn all society into a convent. Shows and entertainments were expressly forbidden by their religion; and for more than two hundred years there was not a single musical instrument allowed in the city of Geneva. They condemned auricular confession, but they enjoined a public one; and in Switzerland, Scotland, and Geneva it was performed the same as penance."

Very little is known about Calvin's personal life in Geneva. His house and furniture were owned by the council. The house was big enough to accommodate his family as well as Antoine's family and some servants. On 28 July 1542, Idelette gave birth to a son, Jacques, but he was born prematurely and survived only briefly. Idelette fell ill in 1545 and died on 29 March 1549. Calvin never married again. He expressed his sorrow in a letter to Viret:

I have been bereaved of the best friend of my life, of one who, if it has been so ordained, would willingly have shared not only my poverty but also my death. During her life she was the faithful helper of my ministry. From her I never experienced the slightest hindrance.

Throughout the rest of his life in Geneva, he maintained several friendships from his early years including Montmor, Cordier, Cop, Farel, Melanchthon and Bullinger.