She was the daughter of Francesco III d'Este, Duke of Modena and Charlotte Aglaé d'Orléans.
Matilde was born in Genoa, the second daughter and fifth child of Francesco III d'Este, Duke of Modena, the sovereign Duke of Modena and his wife, Charlotte Aglaé d'Orléans, Mademoiselle de Valois — a granddaughter of Louis XIV of France and Madame de Montespan.
[1] Her mother separated from her father in the 1740s after an affair with the Duke of Richelieu was discovered at the Modenese court.
Exiled to France, Charlotte Aglaé still managed to arrange the marriages of her daughters.
Her younger sister, Maria Fortunata also married a cousin of theirs, Louis François Joseph de Bourbon, heir to the Prince of Conti.