In 1797 she married her double first cousin Prince Francis, Duke of Calabria, heir to the kingdoms of Naples and Sicily.
She was raised in the Grand Duchy of Tuscany where her father ruled and the family lived until 1790 when, at the death of Maria Clementina's paternal uncle, Joseph II, her father became Emperor of the Holy Roman Empire and the family moved to the court of Vienna.
It was a turbulent period with the Napoleonic wars afflicting the Italian peninsula and the actual wedding did not occur for several years.
In the meantime, both of Maria Clementina's parents died in 1792, in a short period of time, and her brother Francis became the new Emperor.
A frigate picked her up in Trieste, and her new family awaited her at Foggia where the wedding took place on 26 June 1797.
"My son loves her passionately and she reciprocates," wrote the Queen of Naples, her mother-in-law, adding that: "It is a pleasure to see them harmonize so well...
Thanks to my training the young man is very much in love with her as a woman... but this may not last with so much disgust, boredom and no charm of feature, which he is fortunately too nice to notice...
The couple's marital passion astonished the Queen who: "asked heaven to calm their over-excited senses by sending them children".
She is thought to have died from lung disease or tuberculosis, leaving behind her daughter and her devastated husband.
Her only daughter, Maria Carolina, married Charles Ferdinand, Duke of Berry in April 1816.