Anne's energy, strength of will, cunning, and political sense enabled her to overcome the difficulties threatening the kingdom, the most important of which was unrest among the magnates, who had suffered under Louis XI's callous oppressions. Concessions were made: many of Louis's favourites were sacrificed; lands were restored to hostile nobles, among whom was the Duc d'Orléans, the future Louis XII of France; and the States General were convened (1484). When the Beaujeus ignored that assembly's demand to control taxation and hold regular meetings, the “Mad War” broke out between, on the one side, the crown and, on the other, the Duc d'Orléans and Francis II of Brittany, which ended in a royal victory.

In 1491, despite Austrian and English opposition, the Beaujeus concluded the marriage of Charles VIII with Anne of Brittany, which joined the domains of Brittany with the crown. When Charles freed himself from tutelage, however, his former guardians were exposed to the wrath of the new queen, whose duchy's independence had been compromised.

Anne of France had been the dominant party in the Beaujeu marriage. When Pierre died in 1503, Anne remained administrator of his Bourbon lands, protecting them from royal encroachment.