Élisabeth was born in Paris. Her father was César de Bourbon, Duke of Vendôme, legitimised son of King Henry IV of France and his official mistress Gabrielle d'Estrées. Her mother was Princess Françoise of Lorraine (1592–1669), daughter and heiress of Philippe Emmanuel, Duke of Mercœur, himself a rival of Henry IV. Her mother was the Duchess of Mercœur and Penthièvre in her own right and was the greatest heiress of her time.