Francis Bonaventura was born at Château de Sales (Thorens) in Swiss Savoy to a noble family. His father was François de Boisy, a name he took upon receiving the dowry of the Signory de Boisy from Francis' mother, Françoise de Sionnz. Francis was the eldest of twelve children. Early on, he was educated by his mother, and later, by Abbé Deage, his tutor. He loved books and knowledge, and clearly was drawn to things spiritual. He attended the college at Annecy, and there took the tonsure at age 9. His father, in 1578, when he was 12, sent him to the Collège de Clermont at the University of Paris, where he remained for six years. Between 1579 and 1587, Francis suffered from severe scruples and depression resulting in his becoming convinced that he was damned to Hell. He became physically ill and was even bedridden for a time. The intellectual and emotional
At this point he was inspired to visit the shrine of the famous Black Virgin of Paris, Notre-Dame de Bonne-Délivrance.
In 1588, Francis transferred from the University of Paris to the University of Padua in Italy, where he spent four years studying law and theology, earning a doctorate in 1592, which certified him for both. Intelligent and handsome, Francis withstood his father's continual efforts to have him marry and establish a secular career in the Senate of Chambéry, and chose instead a life in religion.
The intervention of Claude de Granier, Bishop of Geneva, led to Francis' ordination as a priest in 1593 and to his appointment as provost of the cathedral chapter of Geneva. Since the beginning of the Protestant Reformation, the seat of the Catholic bishops of Geneva were located at Annecy in Savoy, France, because of Calvinist control of the city of Geneva. Francis, in his capacity as canon provost, engaged in a serious ministry of evangelism among the Protestants of Savoy, apparently persuading many to return to the "Old Faith" (Catholicism).