Villa San Michele is named after the church of St Michael the Archangel. The original building was a monastery, founded in the early years of the 15th century for the Franciscan monks. The land on which it stood had been donated by a Florentine family, the Davanzatis, who also contributed to the monastery's upkeep by gifts of woodlands, further buildings and money.
The present building, with its façade attributed to Michelangelo and its imposing loggia, dates from 1600 when it was enlarged and completely renovated by Giovanni di Bartolommeo Davanzati.
The monastery remained the property of the Franciscans until 1808 when the monastic orders were dissolved by Napoleon and, in 1817, it returned to secular use. By this time, many of its most treasured possessions had been dispersed throughout Florence's churches and art galleries. The triptych in the Academia attributed to Niccolò di Piero Gerini and another above the high altar in the church of Santa Trinità both originally stood in this hilltop sanctuary.