Near the end of 1538, her father and Charles V, Holy Roman Emperor, agreed that Margaret should marry Charles' son, the future Philip II of Spain. However, the agreement between Francis and Charles was short-lived and the marriage never took place.
Shortly before her 36th birthday, a marriage was finally arranged for her by her brother King Henry II of France and her former suitor, Philip II as part of the terms stipulated in the Treaty of Cateau-Cambrésis which was signed by the ambassadors representing the two monarchs on 3 April 1559. The husband selected for her was Philip's ally, Emmanuel Philibert, Duke of Savoy, Prince of Piedmont. At the time, Margaret was described as having been a "spinster lady of excellent breeding and lively intellect".
The wedding took place in tragic circumstances. On 30 June just three days after her marriage contract had been signed, King Henry was gravely injured during a tournament celebrating the wedding of his eldest daughter Elisabeth to the recently widowed King Philip. A lance wielded by his opponent the Count of Montgomery accidentally struck his helmet at a point beneath the visor and shattered. The wooden splinters deeply penetrated his right eye and entered his brain. Close to death, but still conscious, the king ordered that his sister's marriage should take place immediately, for fear that the Duke of Savoy might profit from his death and renege on the alliance.
The ceremony did not take place in Notre Dame Cathedral as had been planned. Instead it was a solemn, subdued event conducted at midnight on 9 July in Saint Paul's, a small church not far from the Tournelles Palace where Margaret's dying brother was ensconced. Among the few guests was the French queen consort Catherine de' Medici who sat by herself, weeping. King Henry died the following day.