As queen-mother she played the part of a mediator between her sons and political parties.
In 1631 Gaston fled to Lorraine and the queen-mother to Brussels.
The queen-mother had at this time fallen in love with Henry Stewart, second son of Lord Avondale, whom she married immediately after obtaining her divorce from Angus in 1527.
At the end of August he appeared before Budapest, the siege of which had already been raised by the defeat of the Austrians; the infant John Sigismund was carried into the sultan's camp, and the queen-mother, Isabella, was peremptorily ordered to evacuate the royal palace, though the sultan gave her a diploma in which he swore only to retain Budapest during the minority of her son.
In this he attracted the favourable attention of Marie de' Medici, the queen-mother, and was chosen at its close to present the address of the clergy embodying its petitions and resolutions.