In his absence, Anna Isabella served as regent, assisted by the Imperial representative Marquis degli Obizzi and some advisers.

She also successfully handled peace negotiations with Spain between the Spanish governor in Milan and the viceroy of Naples, which was concluded in 1692.

In 1702, during the War of the Spanish Succession, Imperiali attacked the Duchy of Mantua, who wished to conquer the areas of Luzzara and Cocoon.

Duke Ferdinando Carlo fled and left Anna Isabella to handle the situation as regent.

She appointed commanders to handle the defense of Luzzara and Cocoon and issued negotiations for Sabbioneta's foreign protection.