On 25 January 1431, Isabella inherited the duchy from her father upon his death, and ruled jointly with her husband as her co-ruler, as was customary for a female monarch at that time.

Her right to rule was questioned by her cousin, Count Antoine de Vaudémont, who captured René in the Battle of Bulgnéville and had him imprisoned with his ally, the Duke of Burgundy.

René appointed her to act as his general governor until his release, and a Napolese embassy asked her to come to Naples to assume the post of regent until her spouse could do so in person.

When Charles VII of France visited in Nancy, they introduced Agnes Sorel to him, who was one of Isabella's ladies-in-waiting.

In July 1445, Isabella appointed her son John to be her governor general in Lorraine, and retired to her manor Launay in Saumur.