 During the eighteen months of the reign of Francis II, Mary encouraged a policy of rounding up French Huguenots on charges of heresy and putting them in front of Catholic judges, and employing torture and burning as punishments for dissenters.Mary returned to Scotland a widow, in the summer of 1561.<ref>Fischer, David Hackett, "Champlain's Dream", 2008, Alfred A. Knopf Canada</ref>

In 1561, the Edict of Orléans declared an end to the persecution, and the Edict of Saint-Germain of January 1562 formally recognised the Huguenots for the first time.However, these measures disguised the growing tensions between Protestants and Catholics.