He was in France in 1745 preparing to help his brother, Prince Charles Edward Stuart (Bonnie Prince Charlie), with the Scottish Jacobite Rebellion. After the suppression of the rebellion, Henry Stuart returned to Italy where he entered the Roman Catholic Church and in 1747 was made a Cardinal. In 1761 he was also made bishop of Frascati, where he lived and worked for years.
As second in line to the throne, on the death of Prince Charles Edward Stuart on January 31, 1788 Henry Stuart became royal claimant as Henry IX. He was the last of the direct male line of James II and the last pretender to lay claim to the English throne.
At the time of the French Revolution he lost his French Royal benefices yet sacrificed many other resources to assist the Pope. He was reduced to poverty by the seizure of his Frascati property by the French. Old and infirm, he fled to Padua and then to Venice. King George III of Great Britain came to his assistance, aiding him with a life-annuity until he was able to return to Frascati in 1800. In return for this kindness the cardinal bequeathed to the Prince of Wales, afterwards George IV of the United Kingdom, the Scottish crown jewels.