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.

Maria was born in Modena to Francesco I d'Este, Duke of Modena and his consort Maria Caterina Farnese. A member of the House of Este, she was a princess of Modena by birth.

In order to cement relations between the House of Farnese, Maria's older sister Isabella d'Este had been married to Ranuccio Farnese, Duke of Parma, son of Odoardo Farnese, Duke of Parma and Margherita de' Medici in 1664. Isabella died in 1666 as a result of childbirth. In order to preserve the union between the two ducal houses, the unmarried Maria became Ranuccio's next consort.

In Modena on 1 October 1668 she was duly married to the widowed Ranuccio Farnese. The marriage produced seven children; she also had two stillborn children. Out of the seven, three survived infancy, however none of them went on to have further children.

Maria died in Parma at the age of 39. Her husband survived her by ten years. Her two youngest sons, Francesco and Antonio, each became the Duke of Parma. Antonio was the last member of the House of Farnese, the duchy of Parma going to the Spanish House of Bourbon in 1731.

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