Her marriage to Francesco I de' Medici, Grand Duke of Tuscany, took place on 18 December 1565 in Florence, after she solemnly arrived in the city by the Porta al Prato. Giorgio Vasari and Vincenzo Borghini, with the help of Giovanni Caccini made big festivities for these event. The party was also taken to the Medici Villa in Poggio a Caiano. Nevertheless, Joanna was homesick and unhappy. Ignored by her husband, and despised by the Florentines for her Austrian hauteur, she never felt at home in Florence. Her father-in-law, Cosimo I de' Medici, was reasonably kind to Joanna. He had the courtyard of the Palazzo Vecchio specially decorated for her; the lunettes were painted with murals of Austrian towns by pupils of Vasari, and Verrocchio's Putto with Dolphin fountain was brought down from the Careggi villa where it had been set up in the garden by Lorenzo de' Medici. The position of Joanna in the Florentine court was a difficult one: between 1567 and 1575, she gave birth to six daughters, of whom only three survived infancy. The absence of a male heir to continue the dynasty was the cause of constant conflict with her husband, who preferred the company of his mistress Bianca Cappello, who gave birth to a son, Antonio, in 1576. Finally, in 1577 Joanna gave birth to the long-awaited heir, baptised Filippo in honour of King Philip II of Spain, Joanna's first cousin. The birth was celebrated with great joy by the court, as now the succession of the Grand Duchy was secured and any ambitions of Bianca Cappello to have her son Antonio as heir of Tuscany were eliminated. However Filippo was to die young, and Joanna's brother-in-law, Ferdinando, succeeded Francesco as Grand Duke.
Death
On 10 April 1578, Joanna – heavily pregnant with her eighth child – fell from the stairs in the Grand Ducal Palace in Florence. Some hours later, she prematurely gave birth to a son, who died immediately. She died the next day on 11 April. Francesco subsequently married his mistress, Bianca Cappello, making her grand duchess. The mysterious circumstances around this accident caused rumours accusing her husband and his mistress of murdering her, so that they could be married. However, modern medical investigation of her remains confirm the official reports of her death as caused by the birth. Joanna suffered from scoliosis: her spine and pelvis were severely deformed. It is clear from the condition of her pelvis that her previous births had been difficult, and it seems remarkable that she had survived them.