She was still an infant when her father and older sister, Leopoldina, died within a month of one another in 1693.

Her mother, a wealthy widow, was married for a second time, against her wishes, on 2 July 1697 in Düsseldorf to Prince Gian Gastone de' Medici, a younger son of the Grand Duke of Tuscany, to whom she brought the prospect of inheriting substantial lands in Bohemia.

Rather than dwelling in her father-in-law's capital, Florence, the couple initially took up residence at his wife's Bohemian domain, the castle of Ploskovice near Reichstadt.

In less than a year Gian Gastone left his wife for Prague, thence resuming residence in Florence, and the couple never again cohabited.

In 1723 Maria Anna's stepfather became Grand Duke Gian Gastone of Tuscany, succeeding his elder brother, and her mother became Grand Duchess of Tuscany, although she never set foot in her husband's realm.