Only once, in 1552, during the invasion of the Tyrol by the Protestant army under the command of Maurice, Elector of Saxony, did Joanna and her sisters Magdalena, Margaret, Barbara and Helena, spend some time outside the monastery at Bruneck Castle.

This involved a procession of gods and godesses alluding to the union between Joanna and Francesco being likened to the wedding of Peleus and Thetis[4].The party was also taken to the Medici villa in Poggio a Caiano.

Her new husband who was of a taciturn and secretive character was noted to "set little store in virtue"[5] was a womanizer who ignored Joanna and instead occupied himself with his mistress Bianca Cappello.

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 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.

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, modern medical investigation of her remains confirm the official reports of her death as caused by the birth (the child presented arm first, and Joanna suffered a ruptured uterus).