Marriage
In 1560, Barbara was considered as a wife for Guglielmo Gonzaga, Duke of Mantua, who later married Eleanor, Barbara's elder sister. In 1562, several suitors came to Emperor Ferdinand I to ask for the hand of his youngest daughter Joanna, among them John Sigismund Zápolya, Francesco de' Medici, Crown Prince of Florence and Alfonso II d'Este, Duke of Ferrara, Modena and Reggio. Alfonso II began negotiations for marriage in November 1563.
A dynastic marriage with the head of the House of Este was beneficial to the House of Habsburg, who sought to reduce the traditional influence of the French kings over the dukes of Ferrara. However, in order to avoid a conflict between the Houses of Medici and Este, the Emperor proposed that Barbara marry Alfonso II. This decision was supported by King Philip II of Spain, an ally of the Duchy of Florence.
Barbara first met Alfonso II in July 1565, when he visited Innsbruck to get to know her. In November of the same year, she and Joanna arrived in Trento, where Pope Pius IV sent his legates to conduct a double marriage ceremony, Joanna to Francesco de' Medici and Barbara to Alfonso d'Este. The ceremony was postponed due to a quarrel between the grooms-to-be over who had precedence in the ceremony. In the end, the brides went separately to the respective capitals of their future spouses (Florence and Ferrara) to marry.
On 1 December 1565, Barbara arrived in Ferrara, and on 5 December she was married to Alfonso II, Duke of Ferrara, Modena and Reggio. The wedding celebrations, during which a "Temple of Love" was built and a grand tournament took place, lasted until 9 December. Among the guests at the wedding were the former fiancé of Barbara, the Duke of Mantua, with his wife, her older sister. Torquato Tasso (at that time the court poet of the Dukes of Ferrara) was a witness to the solemn entry of the bride's procession to Ferrara and subsequent wedding; he later described what he saw in his pastoral drama "Aminta", in which he dedicated several canzones in praise of Barbara. The celebrations were cut short because of the death of Pope Pius IV.
On becoming duchess of Ferrara, Barbara won the love of her subjects through the merciful way in which she treated all those in need. Despite her not speaking Italian, she and her husband enjoyed a complete understanding. Their marriage, which proved childless, was happy. When, a year after the wedding, Alfonso II participated in the war against the Ottoman Empire, Barbara was sincerely worried about her husband. The experience negatively impaired her health; from that time she was reported as being constantly ill.
Despite being a devout Catholic, Barbara was able to forge an excellent relationship with her Protestant mother-in-law Renée of France. The Duchess's confessors in Ferrara, as well as in Innsbruck, were Jesuits, to whom Barbara provided special patronage. After the devastating earthquakes in 1570 and 1571 in the Duchy of Ferrara, she supported young orphaned girls. To this end, she founded the Conservatore delle orfane di Santa Barbara in Ferrara. In the period between earthquakes, the Duchess herself was forced to live in a tent, which exacerbated her health problems.