Only a few days later, the death of Emperor Francis made Maria Luisa's husband the new Grand Duke of Tuscany, and the newly married couple moved to Florence, where they would live for the next twenty-five years.

She accepted the infidelities of her spouse without complaint: among his best known lovers were Lady Anna Gore Cowper, and another was the ballerina Livia Raimondi, with whom he had a son, Luigi von Grün (1788–1814), and he gave her her own palace at Piazza San Marco, Florence.

As grand duchess of Tuscany, Maria Luisa made herself appreciated in the first year in Florence, during the famine of 1765, when she provided the poor and needing with food and medical aid, and she was referred to as an ideal "model of feminine virtue".

Taking the name of Leopold II, the new emperor moved his family to Vienna, where Maria Luisa took on the role of imperial consort, being the penultimate Holy Roman Empress and the last to have had held the title until her husband's death.

Maria Luisa is one of those 41 people who received a "Separated Funeral" with a division of the body into all three traditional Viennese burial places of the Habsburgs (Imperial Crypt, Herzgruft, Herzogsgruft).

In musical circles, Maria Luisa is famous for her putative denigration of Mozart's opera, which she supposedly dismissed as "una porcheria tedesca" (Italian for "German rubbish"), however no claim that she made this remark pre-dates the publication in 1871 of Alfred Meissner's Rococo-Bilder: nach Aufzeichnungen meines Grossvaters, a collection of stories about cultural and political life in Prague in the late eighteenth and early nineteenth centuries.