Born in Florence, Francesco was the son of Cosimo I de' Medici, Grand Duke of Tuscany, and Eleanor of Toledo.

On 18 December 1565, Francesco married Archduchess Joanna of Austria, youngest daughter of Ferdinand I, Holy Roman Emperor and his wife Anne of Bohemia and Hungary.

[3] Soon after Grand Duchess Joanna had died, Francesco went on to marry his Venetian mistress, Bianca Cappello, after aptly disposing of her husband, a Florentine bureaucrat.

He continued his father's patronage of the arts, supporting artists and building the Medici Theater as well as founding the Accademia della Crusca.

Although the original death certificates mention malaria, it has been widely speculated that the couple was poisoned, possibly by Francesco's brother Ferdinando.

The painter Giuseppe Moricci attended the ceremony and depicted Francesco with a facial droop, a right claw hand appearance, the right shoulder internally rotated, the right calf muscle wasted and a right clubfoot confirmed by orthopaedic footwear within the coffin.