The Church of San Michele was built in Anacapri on the initiative of Mother Serafina di Dio, a nun from Capri who had earlier founded a convent of the Order of St Teresa.

The convent was created on the site of an earlier a music conservatory. It was modified at the end of the 17th century to accommodate a group of nuns bound by a vow of strict seclusion.

During the British occupation of Capri, from May 1806 to October 1808, the Governor-General Hudson Lowe authorised the use of some of the rooms as an armoury. When the island was taken by the French, the new Governor Jean Thomas ordered the suppression of religious orders and monasteries, and the nuns were forced to leave Anacapri. The convent was eventually sold and became a military orphanage, and later became the property of Count Von Poppenheim, a German. In 1880, it was seized from the count and sold to a private individual.

King Ferdinando I of Bourbon rediscovered the church during his reign. He had it reopened for religious services and then donated it to the Lay Congregation of the Immaculate Conception.

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