She was a daughter of Francesco I d'Este, Duke of Modena and Maria Caterina Farnese.

[1] Maria was the eighth child and fourth daughter of Francesco I d'Este, the reigning Duke of Modena since 1629.

Her mother was a daughter of Ranuccio I Farnese, Duke of Parma.

[2] In order to preserve the union between the two ducal houses, the unmarried Maria became Ranuccio's next consort.

A wedding was signed by proxies in October 1667 and formally in Modena on 1 January 1668 she was duly married to the widowed Ranuccio Farnese.