The monastery was and still is today one of the Vallombrosa Congregation’s most important institutions. The founder of the Order, St. Giovanni Gualberto, traditionally held to come from the nearby Castle of Petroio, spent the last years of his life and was buried here.
Of the ancient 11th-century church, only the crypt remains, the rest having been rebuilt in the early 13th century. Renaissance elements deriving from 15th-century restoration can be seen in the chapter room, the cloister and the refectory, with a Last Supper frescoed by Domenico and David Ghirlandaio. The church was remodelled in the 16th century, when the screen with the altar pieces by Michele and Ridolfo del Ghirlandaio was added; the Chapel of St. Giovanni Gualberto was redecorated, along with the presbytery, with works by the sculptor Giovanni Caccini and the painter Alessandro Allori and assistants. In the main chapel of San Michele Arcangelo, Domenico Cresti, known as Passignano, provided the frescoed decoration and three altarpieces.
After the 19th-century suppressions of the religious orders, the Badia was acquired by the Polish family Dzieduszycki, who added neo-Gothic elements in the late 19th century. The Vallombrosans returned to the monastery only in 1986.