Marcantonio Maffei was born in Bergamo on November 29, 1521, the son of nobles Girolamo Maffei and Antonia Mattei. His older brother Bernardino Maffei was also a cardinal, and his nephews Orazio Maffei and Marcello Lante.
He was educated at the University of Ferrara, becoming a doctor of both laws in September 1547. He then moved to Rome and in 1549, became a consistorial lawyer. He also became a canon of the Archbasilica of St. John Lateran. In 1552, he was vice-governor of Viterbo.
Archbishop of Chieti
He was elected Archbishop of Chieti on July 14, 1553; he succeeded his brother Barnardino Maffei as archbishop. Around 1554, he became a Referendary of the Apostolic Signatura. He was the Governor of Viterbo from September 27, 1555 until 1557. From 1560 until January 1566, he was the vicegerent of the Vicar General of Rome; he later served as Vicar General of Rome. Pope Pius V made him his nuncio before the Kingdom of Poland. In 1566, he was appointed Datary of His Holiness, maintaining that position until 1570. Sometime before January 14, 1568, he resigned the administration of his archbishopric. Following the death of Maffei's brother Achille, Maffei was given his canonry in St. Peter's Basilica on July 29, 1568. He became a Domestic Chaplain of His Holiness in October 1569.