Known as Mademoiselle d'Alençon until her marriage, Isabelle (Élisabeth Marguerite) was acquainted with the young Louise Françoise de La Baume Le Blanc, who was to become duchesse de La Vallière, mistress of Louis XIV, and who grew up at Blois in the entourage of Isabelle's sister Marguerite Louise d'Orléans.

Her brief union with the Duke of Guise produced one child: Isabelle's husband died in 1671, from smallpox contacted on his way back from a visit to the court of Charles II, King of England.

[6] After the death of her son, Isabelle (whom the French knew as "Madame de Guise") spent every summer in her duchy of Alençon and most winters at the royal court.

After 1675, this little circle expanded when Isabelle's sister Marguerite Louise, Grand Duchess of Tuscany, left her husband, moved into an apartment within the abbey walls, and was kept under what amounted to house arrest.

Isabelle was a fervent supporter of her cousin Louis XIV's policies to bring Huguenots back into the Catholic fold.

As early as November 1676, when she supervised the conversion of a Protestant lady, Isabelle commissioned from Marc-Antoine Charpentier the first of a succession of oratorios that recounted how St. Cecilia had won over her bridegroom and his brother to Christianity.

The fortune that she had accumulated was willed to her older and only surviving sibling, Marguerite Louise, Grand Duchess of Tuscany.