Marie Julie Clary was born in Marseille, France, the daughter of François Clary (Marseille, St Ferreol, 24 February 1725 – Marseille, 20 January 1794), a wealthy silk manufacturer and merchant of Irish heritage, and his second wife (married on 26 June 1759) Françoise Rose Somis (Marseille, St. Ferreol, 30 August 1737 – Paris, 28 January 1815). Her sister Désirée Clary, six years younger, became Queen of Sweden and Norway when her husband, Marshal Bernadotte, was crowned King Charles XIV John of Sweden (Charles III John of Norway). Their brother, Nicholas Joseph Clary, was created 1st Comte Clary and married Anne Jeanne Rouyer (their granddaughter would be the first wife of Joachim, 4th Prince Murat).
On 1 August 1794, at Cuges (Bouches-du-Rhône department), she married Joseph Bonaparte, elder brother of Napoléon Bonaparte. She accompanied her spouse to Italy when he became ambassador to Rome in 1797, and then settled with him in Paris in 1800.
In 1804, when her brother-in-law Napoleon made himself emperor, he named his brother Joseph Imperial Prince, giving Julie status of Imperial Princess. During the coronation of the emperor and empress the same year, Julie was given the task to carry the train of the empress with her sisters-in-law.
Julie was reportedly very capable to behave in accordance with court etiquette and "royal formality", but she preferred to live a private life surrounded by her family and relatives in her chateau in Mortefontaine, Oise (which had been bought in 1800), away from court as well as away from her adulterous spouse.
Joseph was made King of Naples in 1806, thereby making Julie queen consort of Naples. She preferred to stay separated from him in Mortefontaine, however, and was ceremoniously treated as queen in the Imperial court of Paris. She finally joined Joseph in Naples before April 1808, when she was sent there by Napoleon to support him, as he by that time faced a rebellion. When they left, the Napolitans were convinced that they had removed many valuables with them, and commented: "The King arrived like a sovereign, and left like a brigand. The Queen arrived in rags and left like a sovereign."
In 1808, Joseph was made King of Spain and Julie thereby formally became Queen of Spain. She was the first queen of Spain not of royal birth. However, she did not join him when he traveled to Spain and in fact never lived there, preferring to remain in her residence in Mortefontaine. She was kept informed from Vichy and Plombières about her husband's adulterous relationships in Spain. In Spain, she was referred to as "Reina ausente" ('The Absent Queen').
Napoleon's army was defeated at the Battle of Vitoria on 21 June 1813. During the war, Julie gave refuge to her sister Desirée Clary, who by her marriage to the Crown Prince of Sweden was in fact an enemy citizen, as well as her sister-in-law Catharina of Württemberg, in her home Mortefontaine, and when the allied troops took Paris in 1814, Julie herself took refuge in the home of her sister Desirée in Paris.
After the deposition of Napoleon, Julie bought the castle of Prangins in Switzerland, near Lake Léman.
During the Hundred Days in 1815, Julie was among those to welcome Napoleon to the Palace in Paris, dressed in Imperial court robe, alongside his former stepdaughter Hortense.
After the Battle of Waterloo and the second downfall of Napoleon, the members of the Bonaparte family was exiled, and Joseph bought a property in the State of New Jersey near the River Delaware, with the proceeds of the sale of Spanish paintings taken from ransacked Madrid palaces, castles, monasteries and town halls; Julie herself, however, did not join him there, but left with her daughters to Frankfurt, where she stayed for six years, separated from her French-American husband.
In 1816, her sister Desiree, who was Crown Princess of Sweden, wished to bring Julie with her upon her return to Sweden; her husband the crown prince, however, thought this unwise, as Julie was a member of the Bonaparte family and her presence might be taken as a sign that he sided with the deposed Napoleon, and in the end, this came to nothing.
Julie settled in Brussels in 1821, and then in Florence, Italy, at the Serristori Palace. She did not socialize with the French people. She was described as charming, quiet, dignified and peaceful and generally well liked. In 1823, she parted with her sister Desiree, who, as the Queen of Sweden, moved to Sweden. In 1840, Joseph joined Julie in Florence. In spite of his adultery, she referred to Joseph as "my beloved husband".
Joseph Bonaparte died on 28 July 1844, aged 76. Julie died eight months later in Florence, on 7 April 1845, at the age of seventy-three. They were buried side by side at the Basilica of Santa Croce in Florence. 17 years later, in 1862, the self-proclaimed French Emperor Napoleon III brought Joseph Bonaparte's remains back to France and had them inhumed to the right of his younger brother, the Emperor Napoleon I. The remains of Julie are still at the Basilica of Santa Croce in Florence beside those of her daughter, Charlotte, who died in Lucca, in Italy, on 3 March 1839, aged 37, giving birth to a stillborn child.
Joseph and Julie Bonaparte had three daughters:Julie Joséphine Bonaparte (1796).
Zénaïde Laetitia Julie Bonaparte (1801–1854), had twelve children.
Charlotte Napoléone Bonaparte (1802–1839), married in 1826 Napoléon Louis, eldest son of Louis Bonaparte, King of Holland, and Hortense de Beauharnais, widowed in 1830.