The House of Habsburg ruled the Holy Roman Empire intermittently from 1273 to 1806. In 1477, under pressure from the States, which wished to regain their former prerogatives, Mary of Burgundy enacted the 'Great Privilege'. She was only nineteen and not yet married to Maximilian I. The document provided for the abolition of the Parlement of Mechlin and the central court of audit and their replacement by a new body, the Great Council of Mechlin. From now on, the States General and the states of the different provinces could meet on their own authority. Flanders, Holland, Namur and Brabant received major privileges of their own. These measures prevented the disintegration of the Low Countries.

After the death of Charles the Bold, King Louis XI of France immediately occupied the duchy of Burgundy and sent his army north. In September of the same year, a truce was declared between Mary's husband, Maximilian I of Austria, and Louis XI but in 1478 the French confiscated Charles the Bold's French lands and war broke out again. A victory by Maximilian over the French army guaranteed Mary continued possession of Flanders. When she died in 1482 after falling from her horse, she was succeeded by her three-year-old son Philip the Handsome, with his father Maximilian acting as regent. Flanders and Brabant strongly objected to this regency. They recognised Maximilian only after he had signed the Peace of Arras with France and on condition that his two-year-old daughter married the thirteen-year-old Charles VIII of France. Burgundy was regarded as rightfully belonging to France.

In 1493, Maximilian succeeded his father as Holy Roman Emperor. His son Philip the Handsome, now able to act for himself, took over the government of the Low Countries and married Joan of Castile. When he suddenly died in 1506, his son Charles V was still a child and Maximilian resumed the regency, sending his daughter Margaret of Savoy to Brussels to represent him as governor-general.