Marie Henriette was one of five children from the marriage of Archduke Joseph, Palatine of Hungary, and Duchess Maria Dorothea of Württemberg.

Marie Henriette was a vivid and energetic person with a strong will and a hot temperament, interested in riding.

Leopold was the second-surviving son of Leopold I of Belgium and his French wife, Louise of Orléans; Marie Henriette was the sister-in-law of Charlotte of Belgium, future Empress of Mexico and a cousin by marriage to Victoria of the United Kingdom and Maria II of Portugal.

As the former Protestant monarch of a newly established monarchy, the Belgian king wished his son to marry a member of a Roman Catholic and prestigious dynasty, and the name Habsburg was one of her more important qualities.

The marriage furthermore created a historical link between the new Kingdom of Belgium and the Habsburg dynasty of the Austrian Netherlands.

The marriage was suggested by her future father-in-law the king of Belgium to her guardian, the Archduke John of Austria, and arranged by the two men over her head.

Marie Henriette resigned from her rights to the Austrian throne and signed the marriage contract in Vienna on 8 August 1853.

In April 1854, Leopold and Marie Henriette settled in the Palace of Laeken as duke and duchess of Brabant.

Marie Henriette was given her own household, with her mother-in-law's former Dame d'honneur (principal lady-in-waiting) the comtesse de Mérode.

Marie Henriette and her spouse made a state visit to France to attend the Exposition Universelle (1855).

In 1856, her cousin Archduke Maximilian visited the Belgian court to meet his future wife, Marie Henriette's sister-in-law Charlotte.

He estimated that Marie Henriette must have had help from her lively intelligence to overcome many sensitive situations and that she brought some life to the Belgian royal family.

Both trips were made when Marie Henriette was pregnant, and she expressed her disappointment in being left at home with the children while he was making long journeys to faraway lands.

Charlotte initially stayed with the royal couple at Laeken, where Marie Henriette reportedly hardly left her side and devoted herself to improving her health.

The wedding anniversary of the king and queen in August 1878 was the subject of national celebrations all over Belgium: Festivals were arranged, public buildings decorated and four holidays declared.

Marie Henriette was given a tiara financed by the contributions of citizens through a public committee, and the queen held a patriotic speech in gratitude.

When their son-in-law the Crown prince of Austria committed suicide in the Mayerling incident in 1889, Marie Henriette and Leopold ignored the ban from the Austrian Emperor and attended his funeral.

In 1895 she retreated to Spa; her youngest daughter Clementine replaced her as first lady at the Court in Brussels for the remainder of her husband's life.